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-- *Regards* Garima Singh AcSIR-PhD Fellow Biotechnology Division C/o Dr. Ashok Sharma (Chief Scientist and Head Biotechnology Division) Central Institute Of Medicinal And Aromatic Plant CSIR-CIMAP Lucknow garimabioinfo.gmail.com *INDIA* Please don't print this e-mail unless you really need to. Be Green ! On Wed, Jul 5, 2017 at 12:30 AM, <amber-request.ambermd.org> wrote: > Send AMBER mailing list submissions to > amber.ambermd.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.ambermd.org/mailman/listinfo/amber > or, via email, send a message with subject or body 'help' to > amber-request.ambermd.org > > You can reach the person managing the list at > amber-owner.ambermd.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of AMBER digest..." > > > AMBER Mailing List Digest > > Today's Topics: > > 1. Re: Error with 'surf' and acetonitrile-water solvent mixture > (Daniel Roe) > 2. Re: MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions > 7440 (Andrew Schaub) > 3. Re: MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions > 7440 (Rana Rehan Khalid) > 4. Re: How continue a crached minimization step? (N?bia Prates) > 5. Re: How continue a crached minimization step? (Bill Ross) > 6. xleap editor (Rana Rehan Khalid) > 7. Re: xleap editor (Bill Ross) > 8. Question about installing Amber16 on the intel Xeon phi > computational server (Mingyuan) > 9. Re: Question about installing Amber16 on the intel Xeon phi > computational server (Bill Ross) > 10. Amber md in HPC (Garima Singh) > 11. Re: xleap editor (Rana Rehan Khalid) > 12. Re: Amber md in HPC (Elvis Martis) > 13. Re: xleap editor (Bill Ross) > 14. Re: xleap editor (Elvis Martis) > 15. Re: Amber md in HPC (Bill Ross) > 16. Re: xleap editor (Rana Rehan Khalid) > 17. MPI error when trying to run heating (Daniela Rivas) > 18. Re: MPI error when trying to run heating (Bill Ross) > 19. MCPB.py error step 2 (Lizelle Lubbe) > 20. Re: MPI error when trying to run heating (Daniela Rivas) > 21. Re: MPI error when trying to run heating (Bill Ross) > 22. Reproduction of MMPBSA Calculations on Processed Trajectories > (Guqin Shi) > 23. Re: Amber md in HPC (David Case) > 24. Re: MPI error when trying to run heating (David Case) > 25. Re: How continue a crached minimization step? (N?bia Prates) > 26. Re: MCPB.py error step 2 (Dr. M. Shahid) > 27. Residue number in tleap not appropriate with residue number > in pdb file (NADIA RAHMAH) > 28. Re: How continue a crached minimization step? (Bill Ross) > 29. Re: Residue number in tleap not appropriate with residue > number in pdb file (Bill Ross) > 30. Re: How continue a crached minimization step? (N?bia Prates) > 31. Re: How continue a crached minimization step? (Bill Ross) > 32. RED ESP not working in these days (Rana Rehan Khalid) > 33. Re: RED ESP not working in these days (David Cerutti) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 3 Jul 2017 15:14:26 -0400 > From: Daniel Roe <daniel.r.roe.gmail.com> > Subject: Re: [AMBER] Error with 'surf' and acetonitrile-water solvent > mixture > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > <CAAC0qOastACHNOr-3Nkw8icNuFfCLixWUnT2z62kd7q1Jy > bvNQ.mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Hi, > > It took a while for me to get to it, but this issue in cpptraj is now > fixed in GitHub: https://github.com/Amber-MD/cpptraj/pull/506 > > Thanks again for the report. > > -Dan > > On Fri, May 5, 2017 at 10:43 AM, Marcel Passon <passonmarcel.web.de> > wrote: > > > > Hi, > > > > thank you very much for your advice! Indeed, after stripping the > atoms that > > are not calculated, it worked and I obtained a realistic result (from > 13500 > > to 16900). > > I'll also consider using the 'molsurf' command. > > > > Thanks! > > > > Marcel > > > > Gesendet: Donnerstag, 04. Mai 2017 um 17:54 Uhr > > Von: "Daniel Roe" <daniel.r.roe.gmail.com> > > An: "AMBER Mailing List" <amber.ambermd.org> > > Betreff: Re: [AMBER] Error with 'surf' and acetonitrile-water solvent > > mixture > > PS - You can also try the 'molsurf' command, which uses a better > > procedure for the surface area calculation. > > On Thu, May 4, 2017 at 11:00 AM, Daniel Roe <daniel.r.roe.gmail.com> > wrote: > > > Hi, > > > > > > Thanks for the files. I am seeing some weird behavior of the 'surf' > > > command with them so I think there is a bug lurking in there. For > now > > > a potential workaround may be to 'strip' all atoms you do not want > to > > > calculate the surface area for, e.g. > > > > > > parm HY133_ace_noions.prmtop > > > trajin HY133_ace_noions_prd.nc > > > strip !(:10001-10281) > > > surf out surfACE.dat > > > run > > > > > > Let me know if that helps. In the meantime I'll try to figure out > > > what's going wrong. Thanks for the report, > > > > > > -Dan > > > > > > > > > On Tue, May 2, 2017 at 1:45 PM, Daniel Roe <daniel.r.roe.gmail.com> > wrote: > > >> Hi, > > >> > > >> Unfortunately I'm not able to access the link you posted due to > > >> security restrictions. If the files are not too big can you send > them > > >> to me off-list so I can try to reproduce the issue? Otherwise you > can > > >> post the complete output from cpptraj and I can try to troubleshoot > > >> from there. Thanks, > > >> > > >> -Dan > > >> > > >> On Thu, Apr 27, 2017 at 4:21 AM, Marcel Passon < > passonmarcel.web.de> > > wrote: > > >>> > > >>> Dear Amber users, > > >>> > > >>> > > >>> I?m still not quite familiar with using CPPTRAJ. So I tried to > calculate > > the > > >>> overall SASA of a protein that I?ve simulated in a > solvent-mixture of > > >>> acetonitrile and water with the ?surf? command. Strangely, at the > > beginning > > >>> of the trajectory, the output gave very low areas, that increased > to the > > end > > >>> from 1125 to 14488 (in VMD, the protein doesn?t seem to unfold or > change > > its > > >>> conformation notably). Could this be because the acetonitrile > molecules > > >>> aren?t recognized as solvent (when I did the same in pure water as > > solvent, > > >>> the values remained quite similar)? > > >>> > > >>> > > >>> In my fileshare link you can get the first frame of my > trajectory, its > > >>> parameter file as well as the ?surf? output file for the > simulation in > > the > > >>> solvent mixture (surfACE.dat) and in pure water (surf.dat): > > >>> > > >>> [1][1]http://jmp.sh/b/qmIfZACyYNMwuTqsT6wJ > > >>> > > >>> > > >>> Thank you very much for your help! > > >>> > > >>> References > > >>> > > >>> 1. [2]http://jmp.sh/b/qmIfZACyYNMwuTqsT6wJ > > >>> _______________________________________________ > > >>> AMBER mailing list > > >>> AMBER.ambermd.org > > >>> [3]http://lists.ambermd.org/mailman/listinfo/amber > > >> > > >> > > >> > > >> -- > > >> ------------------------- > > >> Daniel R. Roe > > >> Laboratory of Computational Biology > > >> National Institutes of Health, NHLBI > > >> 5635 Fishers Ln, Rm T900 > > >> Rockville MD, 20852 > > >> [4]https://www.lobos.nih.gov/lcb > > > > > > > > > > > > -- > > > ------------------------- > > > Daniel R. Roe > > > Laboratory of Computational Biology > > > National Institutes of Health, NHLBI > > > 5635 Fishers Ln, Rm T900 > > > Rockville MD, 20852 > > > [5]https://www.lobos.nih.gov/lcb > > -- > > ------------------------- > > Daniel R. Roe > > Laboratory of Computational Biology > > National Institutes of Health, NHLBI > > 5635 Fishers Ln, Rm T900 > > Rockville MD, 20852 > > [6]https://www.lobos.nih.gov/lcb > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > [7]http://lists.ambermd.org/mailman/listinfo/amber > > > > References > > > > 1. http://jmp.sh/b/qmIfZACyYNMwuTqsT6wJ > > 2. http://jmp.sh/b/qmIfZACyYNMwuTqsT6wJ > > 3. http://lists.ambermd.org/mailman/listinfo/amber > > 4. https://www.lobos.nih.gov/lcb > > 5. https://www.lobos.nih.gov/lcb > > 6. https://www.lobos.nih.gov/lcb > > 7. http://lists.ambermd.org/mailman/listinfo/amber > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > -- > ------------------------- > Daniel R. Roe > Laboratory of Computational Biology > National Institutes of Health, NHLBI > 5635 Fishers Ln, Rm T900 > Rockville MD, 20852 > https://www.lobos.nih.gov/lcb > > > > ------------------------------ > > Message: 2 > Date: Mon, 3 Jul 2017 12:18:46 -0700 > From: Andrew Schaub <aschaub.uci.edu> > Subject: Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use > default ions 7440 > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > <CAOmtOhZLWURBai_+70v1uaRycsdRH954jAQHW9CwP2gJUw > sqYQ.mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > I'm confused. Are you trying to do the MCPB approach, or are you trying to > use the heme frcmod/prep file from the paper? Are you attempting to mix > these two approaches? > > I would suggest before trying to run your own system, to run through a > couple of the basic tutorials, as well as the MCPB tutorial. Running > through the tutorials give you an overview of how all of these files are > setup, and how the entire system works. Attempting to run a complex > simulation like heme is not easy, but the tutorails will definitely help. > Please at least do the MCPB tutorial with the model system provided before > trying to load it with a dioxygen or nitric oxide species. You'll save > yourself a lot of time and headaches in the end. > > Good Luck! > > Drew > > On Mon, Jul 3, 2017 at 11:51 AM, Rana Rehan Khalid <rrkhalid.umich.edu> > wrote: > > > i already apply for that. i read the tutorial as you guide me i want to > > know that > > A new atom type definition, if required, must be clear and precise. It > > should also be possible to treat the definition > > in an automatic atom-type assignment procedure. how i can make my pdb > file > > compatible with frcmod and .in file > > I have the force field file frcmod for Heme ---O2 and prep file of it. > and > > i tried manually change my pdb file to make it readable for frcmod and > prep > > file but not succeeded actually i find form many places but i dont know > how > > i use that particular frcmod file and prep file i load these file i > follow > > source leaprc.protein.ff14SB > > source leaprc.gaff > > loadamberparams heme.frcmod > > loadamberprep heme.in > > loadpdb oxyheme.pdb > > tleap aborted with the error like hybridization sp2,sp3 type lines it > maybe > > due to, that my pdb do not match with heme-fe---O2 force field which some > > one send me. > > > > Thanks > > > > On Mon, Jul 3, 2017 at 2:31 PM, Andrew Schaub <aschaub.uci.edu> wrote: > > > > > Rana, > > > > > > You are at the University of Michigan. You guys have Gaussian on the > > > cluster (ARC-TS). You can email them and they will get you set up with > an > > > account and probably show you the basics of running a gaussian job. I > > > assume you are using the same cluster to run your AMBER jobs. > > > > > > Best Regards, > > > > > > Andrew > > > > > > On Mon, Jul 3, 2017 at 11:23 AM, Rana Rehan Khalid <rrkhalid.umich.edu > > > > > wrote: > > > > > > > is there any free tool for QM that uses the MCPB.py output file like > > Go3 > > > > etc > > > > > > > > On Mon, Jul 3, 2017 at 1:05 PM, Pengfei Li < > ambermailpengfei.gmail.com > > > > > > > wrote: > > > > > > > > > Hi Rana, > > > > > > > > > > I think you met similar problem as a former email which you sent to > > me > > > > > independently. The solution is similar. Please let me know your > > trying > > > > and > > > > > difficulties you met to solve the problem. > > > > > > > > > > Kind regards, > > > > > Pengfei > > > > > > > > > > > On Jul 1, 2017, at 8:40 PM, Rana Rehan Khalid < > rrkhalid.umich.edu> > > > > > wrote: > > > > > > > > > > > > after running this command i found this error """MCPB.py -i > > NO.in > > > > -s > > > > > > 1""" > > > > > > Totally there are 313 electrons in the large model. > > > > > > Traceback (most recent call last): > > > > > > File "/home/rehan/Downloads/amber16/bin/MCPB.py", line 562, in > > > > <module> > > > > > > premol2fs, cutoff, watermodel, 2, largeopt, sqmopt, smchg, > > lgchg) > > > > > > File > > > > > > "/home/rehan/Downloads/amber16/lib/python2.7/site- > > > > > packages/mcpb/gene_model_files.py", > > > > > > line 1745, in gene_model_files > > > > > > ionids, chargedict, lgchg, outf, watermodel, largeopt, sqmopt) > > > > > > File > > > > > > "/home/rehan/Downloads/amber16/lib/python2.7/site- > > > > > packages/mcpb/gene_model_files.py", > > > > > > line 1441, in build_large_model > > > > > > chargedict, IonLJParaDict, largeopt) > > > > > > File > > > > > > "/home/rehan/Downloads/amber16/lib/python2.7/site- > > > > > packages/msmtmol/gauio.py", > > > > > > line 156, in write_gau_mkf > > > > > > chg = int(round(chargedict[ionname], 0)) > > > > > > KeyError: 'O02' > > > > > > > > > > > > On Sat, Jul 1, 2017 at 8:57 PM, Andrew Schaub <aschaub.uci.edu> > > > wrote: > > > > > > > > > > > >> You need to add the '-m' flag to specify your multiplicity. > > > Remember, > > > > > >> nitric oxide has one free electron as it's a radical, so it's at > > > > least a > > > > > >> doublet (and not a singlet). So adding '-m 2' would probably fix > > > your > > > > > >> problem. If you are just going to transfer the mol2 to the > MCPB.py > > > > > script > > > > > >> then it's not neccessary to add charges. > > > > > >> > > > > > >> antechamber -fi pdb -fo mol2 -i NIT.pdb -o NIT.mol2 -pf y > > > > > >> > > > > > >> On Sat, Jul 1, 2017 at 5:47 PM, Rana Rehan Khalid < > > > rrkhalid.umich.edu > > > > > > > > > > >> wrote: > > > > > >> > > > > > >>> I tried to produce the mol2 file for Nitric oxide (NO) > following > > > > error > > > > > >> come > > > > > >>> kindly guide me > > > > > >>> antechamber -fi pdb -fo mol2 -i NIT_H_renum.pdb -o NIT.mol2 -c > > bcc > > > > -pf > > > > > y > > > > > >>> -nc 0 > > > > > >>> > > > > > >>> Info: Bond types are assigned for valence state 2 with penalty > > of 3 > > > > > >>> Total number of electrons: 15; net charge: 0 > > > > > >>> INFO: Number of electrons is odd: 15 > > > > > >>> Please check the total charge (-nc flag) and spin > > multiplicity > > > > (-m > > > > > >>> flag) > > > > > >>> > > > > > >>> Running: /home/rehan/Downloads/amber16/bin/sqm -O -i sqm.in -o > > > > sqm.out > > > > > >>> Error: cannot run "/home/rehan/Downloads/amber16/bin/sqm -O -i > > > > sqm.in > > > > > -o > > > > > >>> sqm.out" of bcc() in charge.c properly, exit > > > > > >>> > > > > > >>> On Fri, Jun 30, 2017 at 2:35 AM, Andrew Schaub < > aschaub.uci.edu> > > > > > wrote: > > > > > >>> > > > > > >>>> Are you trying to run two different simulations? One with > nitric > > > > oxide > > > > > >>> (NO) > > > > > >>>> bound? One with dioxygen (O-O) bound? If so, you can just > change > > > an > > > > > >>> oxygen > > > > > >>>> in your dioxygen bound complex to a nitrogen, save that and > run > > > MCPB > > > > > >> ont > > > > > >>>> hat system as well. You would run both simulations, and then > > > compare > > > > > >> the > > > > > >>>> results of the two to look for differences. I believe the > Poulos > > > lab > > > > > >> has > > > > > >>>> done some MD studies on NO in P450s: > > > > > >>>> https://www.ncbi.nlm.nih.gov/pubmed/26448477 > > > > > >>>> https://www.ncbi.nlm.nih.gov/pubmed/27439869 > > > > > >>>> > > > > > >>>> Fortunately heme-bound enzymes are very well studied (for > > example > > > > > >>> myoglobin > > > > > >>>> and hemoglobin), so there is a wealth of information on > > electronic > > > > > >>>> structure calculations and molecular dynamics simulations. > Those > > > two > > > > > >>> review > > > > > >>>> papers I mentioned from ACS Chem Rev is a good place to > start. I > > > > would > > > > > >>>> recommend searching the primary literature to see what > protocols > > > and > > > > > >>>> methods others have used to study heme bound systems to get an > > > idea > > > > of > > > > > >>> what > > > > > >>>> type of analysis or system setups you will need to perform. I > > just > > > > > >> wanted > > > > > >>>> to warn you, I've had limited experience with heme > simulations, > > > and > > > > > >> have > > > > > >>>> found them to be very inflexible, and almost rock-like > compared > > to > > > > > >> other > > > > > >>>> enzymes I have studied in silico. I had to use accelerated > > > sampling > > > > > >>>> techniques to get useful data. > > > > > >>>> > > > > > >>>> Good Luck! > > > > > >>>> > > > > > >>>> Drew > > > > > >>>> > > > > > >>>> On Thu, Jun 29, 2017 at 10:03 PM, Rana Rehan Khalid < > > > > > >> rrkhalid.umich.edu> > > > > > >>>> wrote: > > > > > >>>> > > > > > >>>>> Andrew one more thing i want to ask , i prepare the file for > > heme > > > > > >>>>> containing protein but in our case the heme fe-----NO in one > > > system > > > > > >> and > > > > > >>>>> other it bonded with O2 how i can add it because i need to > > study > > > > when > > > > > >>> NO > > > > > >>>>> attach AND when O2 attach what changes occur so in that case > > how > > > i > > > > > >> add > > > > > >>> NO > > > > > >>>>> and O2 in the system > > > > > >>>>> > > > > > >>>>> On Fri, Jun 30, 2017 at 12:38 AM, Rana Rehan Khalid < > > > > > >>> rrkhalid.umich.edu> > > > > > >>>>> wrote: > > > > > >>>>> > > > > > >>>>>> That's great > > > > > >>>>>> > > > > > >>>>>> On Jun 30, 2017 12:30 AM, "Andrew Schaub" <aschaub.uci.edu> > > > > wrote: > > > > > >>>>>> > > > > > >>>>>>> As Elvis stated. You need Gaussian. But good news, The > > > University > > > > > >> of > > > > > >>>>>>> Michigan has access to it. http://arc-ts.umich.edu/ > > > > > >>> software/gaussian/ > > > > > >>>>>>> > > > > > >>>>>>> Best Regards, > > > > > >>>>>>> > > > > > >>>>>>> Drew > > > > > >>>>>>> > > > > > >>>>>>> > > > > > >>>>>>> On Thu, Jun 29, 2017 at 9:15 PM, Rana Rehan Khalid < > > > > > >>>> rrkhalid.umich.edu> > > > > > >>>>>>> wrote: > > > > > >>>>>>> > > > > > >>>>>>>> this command is not working Andrew i am using amber 16 > is > > > go3 > > > > > >>> not > > > > > >>>>>>> buitin > > > > > >>>>>>>> i have all the input files for this command > > > > > >>>>>>>> > > > > > >>>>>>>> g03 < 4ZF6_small_opt.com > > > > > >>>>>>>> <http://ambermd.org/tutorials/advanced/tutorial20/files/ > > > > > >>>>>>>> mcpbpy_heme/4ZF6_small_opt.com> > > > > > >>>>>>>>> 4ZF6_small_opt.log > > > > > >>>>>>>> > > > > > >>>>>>>> On Thu, Jun 29, 2017 at 11:30 PM, Rana Rehan Khalid < > > > > > >>>>> rrkhalid.umich.edu > > > > > >>>>>>>> > > > > > >>>>>>>> wrote: > > > > > >>>>>>>> > > > > > >>>>>>>>> oh yes it run now. Andrew i use > > > > > >>>>>>>>> > > > > > >>>>>>>>> 2.000000 charge for FE ferrous oxidation state > > > > > >>>>>>>>> > > > > > >>>>>>>>> and use 2.8 cutoff by default from the 4ZF6 < > > > > > >>>>>>>> http://ambermd.org/tutorials/advanced/tutorial20/files/ > > mcpbp > > > > > >>>>>>> y_heme/4ZF6.in>.in > > > > > >>>>>>>> file. is it write ?? > > > > > >>>>>>>>> > > > > > >>>>>>>>> > > > > > >>>>>>>>> On Thu, Jun 29, 2017 at 11:18 PM, Andrew Schaub < > > > > > >>> aschaub.uci.edu> > > > > > >>>>>>> wrote: > > > > > >>>>>>>>> > > > > > >>>>>>>>>> Based off of your output, and lack of an .input file, I > am > > > > > >>>> assuming > > > > > >>>>>>> the > > > > > >>>>>>>>>> following. You most likely copied the input script from > > the > > > > > >>>>> tutorial, > > > > > >>>>>>>> but > > > > > >>>>>>>>>> forgot to change the ions_id. > > > > > >>>>>>>>>> > > > > > >>>>>>>>>> original_pdb 4ZF6_H_renum.pdb > > > > > >>>>>>>>>> group_name 4ZF6 > > > > > >>>>>>>>>> cut_off 2.8 > > > > > >>>>>>>>>> *ion_ids 7440* > > > > > >>>>>>>>>> software_version g09 > > > > > >>>>>>>>>> ion_mol2files FE.mol2 > > > > > >>>>>>>>>> naa_mol2files HEM.mol2 1PE.mol2 EDO.mol2 > > > > > >>>>>>>>>> frcmod_files HEM.frcmod 1PE.frcmod EDO.frcmod > > > > > >>>>>>>>>> > > > > > >>>>>>>>>> If you open up your HNOXO_H_renum.pdb, scroll down to > > where > > > > > >> the > > > > > >>>> Fe > > > > > >>>>>>> is, > > > > > >>>>>>>> and > > > > > >>>>>>>>>> find the atom number. Change your ions_id to match the > > atom > > > > > >>>> number > > > > > >>>>>>>> there. > > > > > >>>>>>>>>> In the original tutorial, the Fe atom ID was pulled from > > > > > >>>>>>>> 4ZF6_H_renum.pdb, > > > > > >>>>>>>>>> by finding this line in the PDB file: > > > > > >>>>>>>>>> > > > > > >>>>>>>>>> HETATM *7440 FE* FE A 462 -7.890 0.888 28.105 > > > > > >> 1.00 > > > > > >>>>>>>>>> 38.80 FE > > > > > >>>>>>>>>> > > > > > >>>>>>>>>> Best Regards, > > > > > >>>>>>>>>> > > > > > >>>>>>>>>> Drew > > > > > >>>>>>>>>> > > > > > >>>>>>>>>> > > > > > >>>>>>>>>> > > > > > >>>>>>>>>> > > > > > >>>>>>>>>> On Thu, Jun 29, 2017 at 7:44 PM, Rana Rehan Khalid < > > > > > >>>>>>> rrkhalid.umich.edu> > > > > > >>>>>>>>>> wrote: > > > > > >>>>>>>>>>> > > > > > >>>>>>>>>>> The following is the input variable you have: > > > > > >>>>>>>>>>> The variable ion_ids is : [7440] > > > > > >>>>>>>>>>> The variable ion_info is : [] > > > > > >>>>>>>>>>> The variable ion_mol2files is : ['FE.mol2'] > > > > > >>>>>>>>>>> The variable original_pdb is : HNOXO_H_renum.pdb > > > > > >>>>>>>>>>> The variable add_bonded_pairs is : [] > > > > > >>>>>>>>>>> The variable additional_resids is : [] > > > > > >>>>>>>>>>> The variable anglefc_avg is : 0 > > > > > >>>>>>>>>>> The variable bondfc_avg is : 0 > > > > > >>>>>>>>>>> The variable cut_off is : 2.8 > > > > > >>>>>>>>>>> The variable chgfix_resids is : [] > > > > > >>>>>>>>>>> The variable force_field is : ff14SB > > > > > >>>>>>>>>>> The variable frcmodfs is : ['HEM.frcmod'] > > > > > >>>>>>>>>>> The variable gaff is : 1 > > > > > >>>>>>>>>>> The variable group_name is : HNOXO > > > > > >>>>>>>>>>> The variable ion_paraset is : CM (Only for nonbonded > > > > > >> model) > > > > > >>>>>>>>>>> The variable large_opt is : 0 > > > > > >>>>>>>>>>> The variable lgmodel_chg is : -99 > > > > > >>>>>>>>>>> -99 means program will assign a charge > > > > > >>>>> automatically. > > > > > >>>>>>>>>>> The variable naa_mol2files is : ['HEM.mol2'] > > > > > >>>>>>>>>>> The variable scale_factor is : 1.0 > > > > > >>>>>>>>>>> ATTENTION: This is the scale factor of > > > > > >>> frequency. > > > > > >>>>> The > > > > > >>>>>>>>>>> force constants will be scaled by > multiplying > > > > > >>> the > > > > > >>>>>>> square > > > > > >>>>>>>>>>> of scale_factor. > > > > > >>>>>>>>>>> The variable smmodel_chg is : -99 > > > > > >>>>>>>>>>> -99 means program will assign a charge > > > > > >>>>> automatically. > > > > > >>>>>>>>>>> The variable software_version is : g09 > > > > > >>>>>>>>>>> The variable sqm_opt is : 0 > > > > > >>>>>>>>>>> The variable water_model is : TIP3P > > > > > >>>>>>>>>>> Traceback (most recent call last): > > > > > >>>>>>>>>>> File "/home/rehan/Downloads/amber16/bin/MCPB.py", > line > > > > > >>> 498, > > > > > >>>> in > > > > > >>>>>>>>>> <module> > > > > > >>>>>>>>>>> addbpairs) > > > > > >>>>>>>>>>> File > > > > > >>>>>>>>>>> > > > > > >>>>>>>>>> "/home/rehan/Downloads/amber16/lib/python2.7/site- > > packages/ > > > > > >>>>>>>>>> mcpb/gene_model_files.py", > > > > > >>>>>>>>>>> line 50, in get_ms_resnames > > > > > >>>>>>>>>>> resid = mol.atoms[i].resid > > > > > >>>>>>>>>>> KeyError: 7440 > > > > > >>>>>>>>>>> _______________________________________________ > > > > > >>>>>>>>>>> AMBER mailing list > > > > > >>>>>>>>>>> AMBER.ambermd.org > > > > > >>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber > > > > > >>>>>>>>>> > > > > > >>>>>>>>>> > > > > > >>>>>>>>>> > > > > > >>>>>>>>>> > > > > > >>>>>>>>>> -- > > > > > >>>>>>>>>> Andrew Schaub > > > > > >>>>>>>>>> Graduate Program in Chemical & Structural Biology > > > > > >>>>>>>>>> Tsai Lab, http:///www.tsailabuci.com/ > > > > > >>>>>>>>>> Luo Lab, http://rayl0.bio.uci.edu/html/ > > > > > >>>>>>>>>> University of California, Irvine > > > > > >>>>>>>>>> Irvine, CA 92697-2280 > > > > > >>>>>>>>>> 949-824-8829 (lab) > > > > > >>>>>>>>>> 949-877-9380 (cell) > > > > > >>>>>>>>>> aschaub.uci.edu > > > > > >>>>>>>>>> _______________________________________________ > > > > > >>>>>>>>>> AMBER mailing list > > > > > >>>>>>>>>> AMBER.ambermd.org > > > > > >>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber > > > > > >>>>>>>>>> > > > > > >>>>>>>>> > > > > > >>>>>>>>> > > > > > >>>>>>>> _______________________________________________ > > > > > >>>>>>>> AMBER mailing list > > > > > >>>>>>>> AMBER.ambermd.org > > > > > >>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber > > > > > >>>>>>>> > > > > > >>>>>>> > > > > > >>>>>>> > > > > > >>>>>>> > > > > > >>>>>>> -- > > > > > >>>>>>> Andrew Schaub > > > > > >>>>>>> Graduate Program in Chemical & Structural Biology > > > > > >>>>>>> Tsai Lab, http:///www.tsailabuci.com/ < > > > > http://www.tsailabuci.com/ > > > > > >>> > > > > > >>>>>>> Luo Lab, http://rayl0.bio.uci.edu/html/ > > > > > >>>>>>> University of California, Irvine > > > > > >>>>>>> Irvine, CA 92697-2280 > > > > > >>>>>>> 949-824-8829 (lab) > > > > > >>>>>>> 949-877-9380 (cell) > > > > > >>>>>>> aschaub.uci.edu <http://www.linkedin.com/pub/ > > > > > >>>> andrew-schaub/9a/907/382/ > > > > > >>>>>> > > > > > >>>>>>> _______________________________________________ > > > > > >>>>>>> AMBER mailing list > > > > > >>>>>>> AMBER.ambermd.org > > > > > >>>>>>> http://lists.ambermd.org/mailman/listinfo/amber > > > > > >>>>>>> > > > > > >>>>>> > > > > > >>>>> _______________________________________________ > > > > > >>>>> AMBER mailing list > > > > > >>>>> AMBER.ambermd.org > > > > > >>>>> http://lists.ambermd.org/mailman/listinfo/amber > > > > > >>>>> > > > > > >>>> > > > > > >>>> > > > > > >>>> > > > > > >>>> -- > > > > > >>>> Andrew Schaub > > > > > >>>> Graduate Program in Chemical & Structural Biology > > > > > >>>> Tsai Lab, http:///www.tsailabuci.com/ < > > http://www.tsailabuci.com/ > > > > > > > > > >>>> Luo Lab, http://rayl0.bio.uci.edu/html/ > > > > > >>>> University of California, Irvine > > > > > >>>> Irvine, CA 92697-2280 > > > > > >>>> 949-824-8829 (lab) > > > > > >>>> 949-877-9380 (cell) > > > > > >>>> aschaub.uci.edu <http://www.linkedin.com/pub/ > > > > > >> andrew-schaub/9a/907/382/> > > > > > >>>> _______________________________________________ > > > > > >>>> AMBER mailing list > > > > > >>>> AMBER.ambermd.org > > > > > >>>> http://lists.ambermd.org/mailman/listinfo/amber > > > > > >>>> > > > > > >>> _______________________________________________ > > > > > >>> AMBER mailing list > > > > > >>> AMBER.ambermd.org > > > > > >>> http://lists.ambermd.org/mailman/listinfo/amber > > > > > >>> > > > > > >> > > > > > >> > > > > > >> > > > > > >> -- > > > > > >> Andrew Schaub > > > > > >> Graduate Program in Chemical & Structural Biology > > > > > >> Tsai Lab, http:///www.tsailabuci.com/ < > http://www.tsailabuci.com/ > > > > > > > > >> Luo Lab, http://rayl0.bio.uci.edu/html/ > > > > > >> University of California, Irvine > > > > > >> Irvine, CA 92697-2280 > > > > > >> 949-824-8829 (lab) > > > > > >> 949-877-9380 (cell) > > > > > >> aschaub.uci.edu <http://www.linkedin.com/pub/ > > > > andrew-schaub/9a/907/382/ > > > > > > > > > > > >> _______________________________________________ > > > > > >> AMBER mailing list > > > > > >> AMBER.ambermd.org > > > > > >> http://lists.ambermd.org/mailman/listinfo/amber > > > > > >> > > > > > > _______________________________________________ > > > > > > AMBER mailing list > > > > > > AMBER.ambermd.org > > > > > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > > > > > > > > > > > _______________________________________________ > > > > > AMBER mailing list > > > > > AMBER.ambermd.org > > > > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > > > > > _______________________________________________ > > > > AMBER mailing list > > > > AMBER.ambermd.org > > > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > > > > > > > > > > > > -- > > > Andrew Schaub > > > Graduate Program in Chemical & Structural Biology > > > Tsai Lab, http:///www.tsailabuci.com/ <http://www.tsailabuci.com/> > > > Luo Lab, http://rayl0.bio.uci.edu/html/ > > > University of California, Irvine > > > Irvine, CA 92697-2280 > > > 949-824-8829 (lab) > > > 949-877-9380 (cell) > > > aschaub.uci.edu <http://www.linkedin.com/pub/ > andrew-schaub/9a/907/382/> > > > _______________________________________________ > > > AMBER mailing list > > > AMBER.ambermd.org > > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > > -- > Andrew Schaub > Graduate Program in Chemical & Structural Biology > Tsai Lab, http:///www.tsailabuci.com/ <http://www.tsailabuci.com/> > Luo Lab, http://rayl0.bio.uci.edu/html/ > University of California, Irvine > Irvine, CA 92697-2280 > 949-824-8829 (lab) > 949-877-9380 (cell) > aschaub.uci.edu <http://www.linkedin.com/pub/andrew-schaub/9a/907/382/> > > > ------------------------------ > > Message: 3 > Date: Mon, 3 Jul 2017 15:30:55 -0400 > From: Rana Rehan Khalid <rrkhalid.umich.edu> > Subject: Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use > default ions 7440 > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > <CAHy_OfNWWwx7tFB=O-Ju7O1wrDyyia5a5oxpne=6GZi_ > gziBKA.mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Yes i read many tutorial and implement but as I told you that someone send > me frcmod and in file that's why I tried to use it may be it works for me > rather then to go for Qm. But now I think should stick with mcpb.py to > prepare file for my system. > > On Jul 3, 2017 3:19 PM, "Andrew Schaub" <aschaub.uci.edu> wrote: > > > I'm confused. Are you trying to do the MCPB approach, or are you trying > to > > use the heme frcmod/prep file from the paper? Are you attempting to mix > > these two approaches? > > > > I would suggest before trying to run your own system, to run through a > > couple of the basic tutorials, as well as the MCPB tutorial. Running > > through the tutorials give you an overview of how all of these files are > > setup, and how the entire system works. Attempting to run a complex > > simulation like heme is not easy, but the tutorails will definitely help. > > Please at least do the MCPB tutorial with the model system provided > before > > trying to load it with a dioxygen or nitric oxide species. You'll save > > yourself a lot of time and headaches in the end. > > > > Good Luck! > > > > Drew > > > > On Mon, Jul 3, 2017 at 11:51 AM, Rana Rehan Khalid <rrkhalid.umich.edu> > > wrote: > > > > > i already apply for that. i read the tutorial as you guide me i want to > > > know that > > > A new atom type definition, if required, must be clear and precise. It > > > should also be possible to treat the definition > > > in an automatic atom-type assignment procedure. how i can make my pdb > > file > > > compatible with frcmod and .in file > > > I have the force field file frcmod for Heme ---O2 and prep file of it. > > and > > > i tried manually change my pdb file to make it readable for frcmod and > > prep > > > file but not succeeded actually i find form many places but i dont know > > how > > > i use that particular frcmod file and prep file i load these file i > > follow > > > source leaprc.protein.ff14SB > > > source leaprc.gaff > > > loadamberparams heme.frcmod > > > loadamberprep heme.in > > > loadpdb oxyheme.pdb > > > tleap aborted with the error like hybridization sp2,sp3 type lines it > > maybe > > > due to, that my pdb do not match with heme-fe---O2 force field which > some > > > one send me. > > > > > > Thanks > > > > > > On Mon, Jul 3, 2017 at 2:31 PM, Andrew Schaub <aschaub.uci.edu> wrote: > > > > > > > Rana, > > > > > > > > You are at the University of Michigan. You guys have Gaussian on the > > > > cluster (ARC-TS). You can email them and they will get you set up > with > > an > > > > account and probably show you the basics of running a gaussian job. I > > > > assume you are using the same cluster to run your AMBER jobs. > > > > > > > > Best Regards, > > > > > > > > Andrew > > > > > > > > On Mon, Jul 3, 2017 at 11:23 AM, Rana Rehan Khalid < > rrkhalid.umich.edu > > > > > > > wrote: > > > > > > > > > is there any free tool for QM that uses the MCPB.py output file > like > > > Go3 > > > > > etc > > > > > > > > > > On Mon, Jul 3, 2017 at 1:05 PM, Pengfei Li < > > ambermailpengfei.gmail.com > > > > > > > > > wrote: > > > > > > > > > > > Hi Rana, > > > > > > > > > > > > I think you met similar problem as a former email which you sent > to > > > me > > > > > > independently. The solution is similar. Please let me know your > > > trying > > > > > and > > > > > > difficulties you met to solve the problem. > > > > > > > > > > > > Kind regards, > > > > > > Pengfei > > > > > > > > > > > > > On Jul 1, 2017, at 8:40 PM, Rana Rehan Khalid < > > rrkhalid.umich.edu> > > > > > > wrote: > > > > > > > > > > > > > > after running this command i found this error """MCPB.py -i > > > NO.in > > > > > -s > > > > > > > 1""" > > > > > > > Totally there are 313 electrons in the large model. > > > > > > > Traceback (most recent call last): > > > > > > > File "/home/rehan/Downloads/amber16/bin/MCPB.py", line 562, > in > > > > > <module> > > > > > > > premol2fs, cutoff, watermodel, 2, largeopt, sqmopt, smchg, > > > lgchg) > > > > > > > File > > > > > > > "/home/rehan/Downloads/amber16/lib/python2.7/site- > > > > > > packages/mcpb/gene_model_files.py", > > > > > > > line 1745, in gene_model_files > > > > > > > ionids, chargedict, lgchg, outf, watermodel, largeopt, > sqmopt) > > > > > > > File > > > > > > > "/home/rehan/Downloads/amber16/lib/python2.7/site- > > > > > > packages/mcpb/gene_model_files.py", > > > > > > > line 1441, in build_large_model > > > > > > > chargedict, IonLJParaDict, largeopt) > > > > > > > File > > > > > > > "/home/rehan/Downloads/amber16/lib/python2.7/site- > > > > > > packages/msmtmol/gauio.py", > > > > > > > line 156, in write_gau_mkf > > > > > > > chg = int(round(chargedict[ionname], 0)) > > > > > > > KeyError: 'O02' > > > > > > > > > > > > > > On Sat, Jul 1, 2017 at 8:57 PM, Andrew Schaub <aschaub.uci.edu > > > > > > wrote: > > > > > > > > > > > > > >> You need to add the '-m' flag to specify your multiplicity. > > > > Remember, > > > > > > >> nitric oxide has one free electron as it's a radical, so it's > at > > > > > least a > > > > > > >> doublet (and not a singlet). So adding '-m 2' would probably > fix > > > > your > > > > > > >> problem. If you are just going to transfer the mol2 to the > > MCPB.py > > > > > > script > > > > > > >> then it's not neccessary to add charges. > > > > > > >> > > > > > > >> antechamber -fi pdb -fo mol2 -i NIT.pdb -o NIT.mol2 -pf y > > > > > > >> > > > > > > >> On Sat, Jul 1, 2017 at 5:47 PM, Rana Rehan Khalid < > > > > rrkhalid.umich.edu > > > > > > > > > > > > >> wrote: > > > > > > >> > > > > > > >>> I tried to produce the mol2 file for Nitric oxide (NO) > > following > > > > > error > > > > > > >> come > > > > > > >>> kindly guide me > > > > > > >>> antechamber -fi pdb -fo mol2 -i NIT_H_renum.pdb -o NIT.mol2 > -c > > > bcc > > > > > -pf > > > > > > y > > > > > > >>> -nc 0 > > > > > > >>> > > > > > > >>> Info: Bond types are assigned for valence state 2 with > penalty > > > of 3 > > > > > > >>> Total number of electrons: 15; net charge: 0 > > > > > > >>> INFO: Number of electrons is odd: 15 > > > > > > >>> Please check the total charge (-nc flag) and spin > > > multiplicity > > > > > (-m > > > > > > >>> flag) > > > > > > >>> > > > > > > >>> Running: /home/rehan/Downloads/amber16/bin/sqm -O -i sqm.in > -o > > > > > sqm.out > > > > > > >>> Error: cannot run "/home/rehan/Downloads/amber16/bin/sqm -O > -i > > > > > sqm.in > > > > > > -o > > > > > > >>> sqm.out" of bcc() in charge.c properly, exit > > > > > > >>> > > > > > > >>> On Fri, Jun 30, 2017 at 2:35 AM, Andrew Schaub < > > aschaub.uci.edu> > > > > > > wrote: > > > > > > >>> > > > > > > >>>> Are you trying to run two different simulations? One with > > nitric > > > > > oxide > > > > > > >>> (NO) > > > > > > >>>> bound? One with dioxygen (O-O) bound? If so, you can just > > change > > > > an > > > > > > >>> oxygen > > > > > > >>>> in your dioxygen bound complex to a nitrogen, save that and > > run > > > > MCPB > > > > > > >> ont > > > > > > >>>> hat system as well. You would run both simulations, and then > > > > compare > > > > > > >> the > > > > > > >>>> results of the two to look for differences. I believe the > > Poulos > > > > lab > > > > > > >> has > > > > > > >>>> done some MD studies on NO in P450s: > > > > > > >>>> https://www.ncbi.nlm.nih.gov/pubmed/26448477 > > > > > > >>>> https://www.ncbi.nlm.nih.gov/pubmed/27439869 > > > > > > >>>> > > > > > > >>>> Fortunately heme-bound enzymes are very well studied (for > > > example > > > > > > >>> myoglobin > > > > > > >>>> and hemoglobin), so there is a wealth of information on > > > electronic > > > > > > >>>> structure calculations and molecular dynamics simulations. > > Those > > > > two > > > > > > >>> review > > > > > > >>>> papers I mentioned from ACS Chem Rev is a good place to > > start. I > > > > > would > > > > > > >>>> recommend searching the primary literature to see what > > protocols > > > > and > > > > > > >>>> methods others have used to study heme bound systems to get > an > > > > idea > > > > > of > > > > > > >>> what > > > > > > >>>> type of analysis or system setups you will need to perform. > I > > > just > > > > > > >> wanted > > > > > > >>>> to warn you, I've had limited experience with heme > > simulations, > > > > and > > > > > > >> have > > > > > > >>>> found them to be very inflexible, and almost rock-like > > compared > > > to > > > > > > >> other > > > > > > >>>> enzymes I have studied in silico. I had to use accelerated > > > > sampling > > > > > > >>>> techniques to get useful data. > > > > > > >>>> > > > > > > >>>> Good Luck! > > > > > > >>>> > > > > > > >>>> Drew > > > > > > >>>> > > > > > > >>>> On Thu, Jun 29, 2017 at 10:03 PM, Rana Rehan Khalid < > > > > > > >> rrkhalid.umich.edu> > > > > > > >>>> wrote: > > > > > > >>>> > > > > > > >>>>> Andrew one more thing i want to ask , i prepare the file > for > > > heme > > > > > > >>>>> containing protein but in our case the heme fe-----NO in > one > > > > system > > > > > > >> and > > > > > > >>>>> other it bonded with O2 how i can add it because i need to > > > study > > > > > when > > > > > > >>> NO > > > > > > >>>>> attach AND when O2 attach what changes occur so in that > case > > > how > > > > i > > > > > > >> add > > > > > > >>> NO > > > > > > >>>>> and O2 in the system > > > > > > >>>>> > > > > > > >>>>> On Fri, Jun 30, 2017 at 12:38 AM, Rana Rehan Khalid < > > > > > > >>> rrkhalid.umich.edu> > > > > > > >>>>> wrote: > > > > > > >>>>> > > > > > > >>>>>> That's great > > > > > > >>>>>> > > > > > > >>>>>> On Jun 30, 2017 12:30 AM, "Andrew Schaub" < > aschaub.uci.edu> > > > > > wrote: > > > > > > >>>>>> > > > > > > >>>>>>> As Elvis stated. You need Gaussian. But good news, The > > > > University > > > > > > >> of > > > > > > >>>>>>> Michigan has access to it. http://arc-ts.umich.edu/ > > > > > > >>> software/gaussian/ > > > > > > >>>>>>> > > > > > > >>>>>>> Best Regards, > > > > > > >>>>>>> > > > > > > >>>>>>> Drew > > > > > > >>>>>>> > > > > > > >>>>>>> > > > > > > >>>>>>> On Thu, Jun 29, 2017 at 9:15 PM, Rana Rehan Khalid < > > > > > > >>>> rrkhalid.umich.edu> > > > > > > >>>>>>> wrote: > > > > > > >>>>>>> > > > > > > >>>>>>>> this command is not working Andrew i am using amber 16 > > is > > > > go3 > > > > > > >>> not > > > > > > >>>>>>> buitin > > > > > > >>>>>>>> i have all the input files for this command > > > > > > >>>>>>>> > > > > > > >>>>>>>> g03 < 4ZF6_small_opt.com > > > > > > >>>>>>>> <http://ambermd.org/tutorials/ > advanced/tutorial20/files/ > > > > > > >>>>>>>> mcpbpy_heme/4ZF6_small_opt.com> > > > > > > >>>>>>>>> 4ZF6_small_opt.log > > > > > > >>>>>>>> > > > > > > >>>>>>>> On Thu, Jun 29, 2017 at 11:30 PM, Rana Rehan Khalid < > > > > > > >>>>> rrkhalid.umich.edu > > > > > > >>>>>>>> > > > > > > >>>>>>>> wrote: > > > > > > >>>>>>>> > > > > > > >>>>>>>>> oh yes it run now. Andrew i use > > > > > > >>>>>>>>> > > > > > > >>>>>>>>> 2.000000 charge for FE ferrous oxidation state > > > > > > >>>>>>>>> > > > > > > >>>>>>>>> and use 2.8 cutoff by default from the 4ZF6 < > > > > > > >>>>>>>> http://ambermd.org/tutorials/advanced/tutorial20/files/ > > > mcpbp > > > > > > >>>>>>> y_heme/4ZF6.in>.in > > > > > > >>>>>>>> file. is it write ?? > > > > > > >>>>>>>>> > > > > > > >>>>>>>>> > > > > > > >>>>>>>>> On Thu, Jun 29, 2017 at 11:18 PM, Andrew Schaub < > > > > > > >>> aschaub.uci.edu> > > > > > > >>>>>>> wrote: > > > > > > >>>>>>>>> > > > > > > >>>>>>>>>> Based off of your output, and lack of an .input file, > I > > am > > > > > > >>>> assuming > > > > > > >>>>>>> the > > > > > > >>>>>>>>>> following. You most likely copied the input script > from > > > the > > > > > > >>>>> tutorial, > > > > > > >>>>>>>> but > > > > > > >>>>>>>>>> forgot to change the ions_id. > > > > > > >>>>>>>>>> > > > > > > >>>>>>>>>> original_pdb 4ZF6_H_renum.pdb > > > > > > >>>>>>>>>> group_name 4ZF6 > > > > > > >>>>>>>>>> cut_off 2.8 > > > > > > >>>>>>>>>> *ion_ids 7440* > > > > > > >>>>>>>>>> software_version g09 > > > > > > >>>>>>>>>> ion_mol2files FE.mol2 > > > > > > >>>>>>>>>> naa_mol2files HEM.mol2 1PE.mol2 EDO.mol2 > > > > > > >>>>>>>>>> frcmod_files HEM.frcmod 1PE.frcmod EDO.frcmod > > > > > > >>>>>>>>>> > > > > > > >>>>>>>>>> If you open up your HNOXO_H_renum.pdb, scroll down to > > > where > > > > > > >> the > > > > > > >>>> Fe > > > > > > >>>>>>> is, > > > > > > >>>>>>>> and > > > > > > >>>>>>>>>> find the atom number. Change your ions_id to match the > > > atom > > > > > > >>>> number > > > > > > >>>>>>>> there. > > > > > > >>>>>>>>>> In the original tutorial, the Fe atom ID was pulled > from > > > > > > >>>>>>>> 4ZF6_H_renum.pdb, > > > > > > >>>>>>>>>> by finding this line in the PDB file: > > > > > > >>>>>>>>>> > > > > > > >>>>>>>>>> HETATM *7440 FE* FE A 462 -7.890 0.888 > 28.105 > > > > > > >> 1.00 > > > > > > >>>>>>>>>> 38.80 FE > > > > > > >>>>>>>>>> > > > > > > >>>>>>>>>> Best Regards, > > > > > > >>>>>>>>>> > > > > > > >>>>>>>>>> Drew > > > > > > >>>>>>>>>> > > > > > > >>>>>>>>>> > > > > > > >>>>>>>>>> > > > > > > >>>>>>>>>> > > > > > > >>>>>>>>>> On Thu, Jun 29, 2017 at 7:44 PM, Rana Rehan Khalid < > > > > > > >>>>>>> rrkhalid.umich.edu> > > > > > > >>>>>>>>>> wrote: > > > > > > >>>>>>>>>>> > > > > > > >>>>>>>>>>> The following is the input variable you have: > > > > > > >>>>>>>>>>> The variable ion_ids is : [7440] > > > > > > >>>>>>>>>>> The variable ion_info is : [] > > > > > > >>>>>>>>>>> The variable ion_mol2files is : ['FE.mol2'] > > > > > > >>>>>>>>>>> The variable original_pdb is : HNOXO_H_renum.pdb > > > > > > >>>>>>>>>>> The variable add_bonded_pairs is : [] > > > > > > >>>>>>>>>>> The variable additional_resids is : [] > > > > > > >>>>>>>>>>> The variable anglefc_avg is : 0 > > > > > > >>>>>>>>>>> The variable bondfc_avg is : 0 > > > > > > >>>>>>>>>>> The variable cut_off is : 2.8 > > > > > > >>>>>>>>>>> The variable chgfix_resids is : [] > > > > > > >>>>>>>>>>> The variable force_field is : ff14SB > > > > > > >>>>>>>>>>> The variable frcmodfs is : ['HEM.frcmod'] > > > > > > >>>>>>>>>>> The variable gaff is : 1 > > > > > > >>>>>>>>>>> The variable group_name is : HNOXO > > > > > > >>>>>>>>>>> The variable ion_paraset is : CM (Only for nonbonded > > > > > > >> model) > > > > > > >>>>>>>>>>> The variable large_opt is : 0 > > > > > > >>>>>>>>>>> The variable lgmodel_chg is : -99 > > > > > > >>>>>>>>>>> -99 means program will assign a charge > > > > > > >>>>> automatically. > > > > > > >>>>>>>>>>> The variable naa_mol2files is : ['HEM.mol2'] > > > > > > >>>>>>>>>>> The variable scale_factor is : 1.0 > > > > > > >>>>>>>>>>> ATTENTION: This is the scale factor of > > > > > > >>> frequency. > > > > > > >>>>> The > > > > > > >>>>>>>>>>> force constants will be scaled by > > multiplying > > > > > > >>> the > > > > > > >>>>>>> square > > > > > > >>>>>>>>>>> of scale_factor. > > > > > > >>>>>>>>>>> The variable smmodel_chg is : -99 > > > > > > >>>>>>>>>>> -99 means program will assign a charge > > > > > > >>>>> automatically. > > > > > > >>>>>>>>>>> The variable software_version is : g09 > > > > > > >>>>>>>>>>> The variable sqm_opt is : 0 > > > > > > >>>>>>>>>>> The variable water_model is : TIP3P > > > > > > >>>>>>>>>>> Traceback (most recent call last): > > > > > > >>>>>>>>>>> File "/home/rehan/Downloads/amber16/bin/MCPB.py", > > line > > > > > > >>> 498, > > > > > > >>>> in > > > > > > >>>>>>>>>> <module> > > > > > > >>>>>>>>>>> addbpairs) > > > > > > >>>>>>>>>>> File > > > > > > >>>>>>>>>>> > > > > > > >>>>>>>>>> "/home/rehan/Downloads/amber16/lib/python2.7/site- > > > packages/ > > > > > > >>>>>>>>>> mcpb/gene_model_files.py", > > > > > > >>>>>>>>>>> line 50, in get_ms_resnames > > > > > > >>>>>>>>>>> resid = mol.atoms[i].resid > > > > > > >>>>>>>>>>> KeyError: 7440 > > > > > > >>>>>>>>>>> _______________________________________________ > > > > > > >>>>>>>>>>> AMBER mailing list > > > > > > >>>>>>>>>>> AMBER.ambermd.org > > > > > > >>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber > > > > > > >>>>>>>>>> > > > > > > >>>>>>>>>> > > > > > > >>>>>>>>>> > > > > > > >>>>>>>>>> > > > > > > >>>>>>>>>> -- > > > > > > >>>>>>>>>> Andrew Schaub > > > > > > >>>>>>>>>> Graduate Program in Chemical & Structural Biology > > > > > > >>>>>>>>>> Tsai Lab, http:///www.tsailabuci.com/ > > > > > > >>>>>>>>>> Luo Lab, http://rayl0.bio.uci.edu/html/ > > > > > > >>>>>>>>>> University of California, Irvine > > > > > > >>>>>>>>>> Irvine, CA 92697-2280 > > > > > > >>>>>>>>>> 949-824-8829 (lab) > > > > > > >>>>>>>>>> 949-877-9380 (cell) > > > > > > >>>>>>>>>> aschaub.uci.edu > > > > > > >>>>>>>>>> _______________________________________________ > > > > > > >>>>>>>>>> AMBER mailing list > > > > > > >>>>>>>>>> AMBER.ambermd.org > > > > > > >>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber > > > > > > >>>>>>>>>> > > > > > > >>>>>>>>> > > > > > > >>>>>>>>> > > > > > > >>>>>>>> _______________________________________________ > > > > > > >>>>>>>> AMBER mailing list > > > > > > >>>>>>>> AMBER.ambermd.org > > > > > > >>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber > > > > > > >>>>>>>> > > > > > > >>>>>>> > > > > > > >>>>>>> > > > > > > >>>>>>> > > > > > > >>>>>>> -- > > > > > > >>>>>>> Andrew Schaub > > > > > > >>>>>>> Graduate Program in Chemical & Structural Biology > > > > > > >>>>>>> Tsai Lab, http:///www.tsailabuci.com/ < > > > > > http://www.tsailabuci.com/ > > > > > > >>> > > > > > > >>>>>>> Luo Lab, http://rayl0.bio.uci.edu/html/ > > > > > > >>>>>>> University of California, Irvine > > > > > > >>>>>>> Irvine, CA 92697-2280 > > > > > > >>>>>>> 949-824-8829 (lab) > > > > > > >>>>>>> 949-877-9380 (cell) > > > > > > >>>>>>> aschaub.uci.edu <http://www.linkedin.com/pub/ > > > > > > >>>> andrew-schaub/9a/907/382/ > > > > > > >>>>>> > > > > > > >>>>>>> _______________________________________________ > > > > > > >>>>>>> AMBER mailing list > > > > > > >>>>>>> AMBER.ambermd.org > > > > > > >>>>>>> http://lists.ambermd.org/mailman/listinfo/amber > > > > > > >>>>>>> > > > > > > >>>>>> > > > > > > >>>>> _______________________________________________ > > > > > > >>>>> AMBER mailing list > > > > > > >>>>> AMBER.ambermd.org > > > > > > >>>>> http://lists.ambermd.org/mailman/listinfo/amber > > > > > > >>>>> > > > > > > >>>> > > > > > > >>>> > > > > > > >>>> > > > > > > >>>> -- > > > > > > >>>> Andrew Schaub > > > > > > >>>> Graduate Program in Chemical & Structural Biology > > > > > > >>>> Tsai Lab, http:///www.tsailabuci.com/ < > > > http://www.tsailabuci.com/ > > > > > > > > > > > >>>> Luo Lab, http://rayl0.bio.uci.edu/html/ > > > > > > >>>> University of California, Irvine > > > > > > >>>> Irvine, CA 92697-2280 > > > > > > >>>> 949-824-8829 (lab) > > > > > > >>>> 949-877-9380 (cell) > > > > > > >>>> aschaub.uci.edu <http://www.linkedin.com/pub/ > > > > > > >> andrew-schaub/9a/907/382/> > > > > > > >>>> _______________________________________________ > > > > > > >>>> AMBER mailing list > > > > > > >>>> AMBER.ambermd.org > > > > > > >>>> http://lists.ambermd.org/mailman/listinfo/amber > > > > > > >>>> > > > > > > >>> _______________________________________________ > > > > > > >>> AMBER mailing list > > > > > > >>> AMBER.ambermd.org > > > > > > >>> http://lists.ambermd.org/mailman/listinfo/amber > > > > > > >>> > > > > > > >> > > > > > > >> > > > > > > >> > > > > > > >> -- > > > > > > >> Andrew Schaub > > > > > > >> Graduate Program in Chemical & Structural Biology > > > > > > >> Tsai Lab, http:///www.tsailabuci.com/ < > > http://www.tsailabuci.com/ > > > > > > > > > > >> Luo Lab, http://rayl0.bio.uci.edu/html/ > > > > > > >> University of California, Irvine > > > > > > >> Irvine, CA 92697-2280 > > > > > > >> 949-824-8829 (lab) > > > > > > >> 949-877-9380 (cell) > > > > > > >> aschaub.uci.edu <http://www.linkedin.com/pub/ > > > > > andrew-schaub/9a/907/382/ > > > > > > > > > > > > > >> _______________________________________________ > > > > > > >> AMBER mailing list > > > > > > >> AMBER.ambermd.org > > > > > > >> http://lists.ambermd.org/mailman/listinfo/amber > > > > > > >> > > > > > > > _______________________________________________ > > > > > > > AMBER mailing list > > > > > > > AMBER.ambermd.org > > > > > > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > AMBER mailing list > > > > > > AMBER.ambermd.org > > > > > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > > > > > > > _______________________________________________ > > > > > AMBER mailing list > > > > > AMBER.ambermd.org > > > > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > > > > > > > > > > > > > > > > > -- > > > > Andrew Schaub > > > > Graduate Program in Chemical & Structural Biology > > > > Tsai Lab, http:///www.tsailabuci.com/ <http://www.tsailabuci.com/> > > > > Luo Lab, http://rayl0.bio.uci.edu/html/ > > > > University of California, Irvine > > > > Irvine, CA 92697-2280 > > > > 949-824-8829 (lab) > > > > 949-877-9380 (cell) > > > > aschaub.uci.edu <http://www.linkedin.com/pub/ > > andrew-schaub/9a/907/382/> > > > > _______________________________________________ > > > > AMBER mailing list > > > > AMBER.ambermd.org > > > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > > > _______________________________________________ > > > AMBER mailing list > > > AMBER.ambermd.org > > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > > > > > > > -- > > Andrew Schaub > > Graduate Program in Chemical & Structural Biology > > Tsai Lab, http:///www.tsailabuci.com/ <http://www.tsailabuci.com/> > > Luo Lab, http://rayl0.bio.uci.edu/html/ > > University of California, Irvine > > Irvine, CA 92697-2280 > > 949-824-8829 (lab) > > 949-877-9380 (cell) > > aschaub.uci.edu <http://www.linkedin.com/pub/andrew-schaub/9a/907/382/> > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > ------------------------------ > > Message: 4 > Date: Mon, 3 Jul 2017 19:11:50 +0000 > From: N?bia Prates <nnubiaits.hotmail.com> > Subject: Re: [AMBER] How continue a crached minimization step? > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > <BLUPR19MB000157F5F1E1EE7F2CB45FE3BED60.BLUPR19MB0001. > namprd19.prod.outlook.com> > > Content-Type: text/plain; charset="iso-8859-1" > > Thank you Elvis and Bill, > > > Now I am heaving the same trouble during the equilibration. > > Can you help me with that? > > > Best > > N?bia > > > ________________________________ > De: Bill Ross <ross.cgl.ucsf.edu> > Enviado: segunda-feira, 3 de julho de 2017 15:21 > Para: amber.ambermd.org > Assunto: Re: [AMBER] How continue a crached minimization step? > > Usually minimization is not worth running at much length, if it is to > prepare for dynamics. I would try about 5-30 minutes of wallclock time > total, so a crash shouldn't matter. Plot the total energy to see what I > mean. > > Bill > > On 7/3/17 7:38 AM, N?bia Prates wrote: > > Hello, > > > > I was running a minimization, but it was not completed due to lack of > power. I was wonder if it is possible to continue minimizing where it > stopped or I have to do another? > > > > > > Best > > > > N?bia > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > lists.ambermd.org > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > lists.ambermd.org > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > > ------------------------------ > > Message: 5 > Date: Mon, 3 Jul 2017 13:50:52 -0700 > From: Bill Ross <ross.cgl.ucsf.edu> > Subject: Re: [AMBER] How continue a crached minimization step? > To: amber.ambermd.org > Message-ID: <6c45dd86-3ec2-e9b4-a730-3e1c39f804d6.cgl.ucsf.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > It sounds like your machine didn't crash, your simulation did? > > If you are having problems with a simulation getting started, best to > paste the .in file (might as well start with the minimization) into your > mail, along with the part of the output indicating failure. > > Bill > > > On 7/3/17 12:11 PM, N?bia Prates wrote: > > Thank you Elvis and Bill, > > > > > > Now I am heaving the same trouble during the equilibration. > > > > Can you help me with that? > > > > > > Best > > > > N?bia > > > > > > ________________________________ > > De: Bill Ross <ross.cgl.ucsf.edu> > > Enviado: segunda-feira, 3 de julho de 2017 15:21 > > Para: amber.ambermd.org > > Assunto: Re: [AMBER] How continue a crached minimization step? > > > > Usually minimization is not worth running at much length, if it is to > > prepare for dynamics. I would try about 5-30 minutes of wallclock time > > total, so a crash shouldn't matter. Plot the total energy to see what I > > mean. > > > > Bill > > > > On 7/3/17 7:38 AM, N?bia Prates wrote: > >> Hello, > >> > >> I was running a minimization, but it was not completed due to lack of > power. I was wonder if it is possible to continue minimizing where it > stopped or I have to do another? > >> > >> > >> Best > >> > >> N?bia > >> > >> _______________________________________________ > >> AMBER mailing list > >> AMBER.ambermd.org > >> http://lists.ambermd.org/mailman/listinfo/amber > > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > > lists.ambermd.org > > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > > lists.ambermd.org > > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > > > ------------------------------ > > Message: 6 > Date: Tue, 4 Jul 2017 00:42:46 -0400 > From: Rana Rehan Khalid <rrkhalid.umich.edu> > Subject: [AMBER] xleap editor > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > <CAHy_OfMHpeL3gtXri0KqDH989HiAxL5uxAUWXfoAt0BKr9Z6NA.mail.gmail. > com> > Content-Type: text/plain; charset="UTF-8" > > Hi everyone > > I want to Know how we use xleap unit editor it consist three buttons like > unit, edit and display button when i want to choose any option among these > button it display the options of that button like unit -----check unit, > calculate charge etc. only for the time until i keep pressing the mouse > left button and when i trying to select any of the option the drop down > menu of that button disappear when i left the mouse button. kindly tell me > thanks > > > ------------------------------ > > Message: 7 > Date: Mon, 3 Jul 2017 23:25:41 -0700 > From: Bill Ross <ross.cgl.ucsf.edu> > Subject: Re: [AMBER] xleap editor > To: amber.ambermd.org > Message-ID: <7e361f42-6ba5-0a69-5482-5ea234d6dccf.cgl.ucsf.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > Is your NumLock key set, by any chance? There is some other unexplained > behavior when that is the case, I believe. > > Bill > > > On 7/3/17 9:42 PM, Rana Rehan Khalid wrote: > > Hi everyone > > > > I want to Know how we use xleap unit editor it consist three buttons like > > unit, edit and display button when i want to choose any option among > these > > button it display the options of that button like unit -----check unit, > > calculate charge etc. only for the time until i keep pressing the mouse > > left button and when i trying to select any of the option the drop down > > menu of that button disappear when i left the mouse button. kindly tell > me > > thanks > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > ------------------------------ > > Message: 8 > Date: Tue, 4 Jul 2017 14:44:32 +0800 > From: "Mingyuan" <ming_yxu.163.com> > Subject: [AMBER] Question about installing Amber16 on the intel Xeon > phi computational server > To: <amber.ambermd.org> > Message-ID: <006101d2f490$fe505070$faf0f150$.163.com> > Content-Type: text/plain; charset="us-ascii" > > Dear Amber group: > > I meet some problem when I tried to install Amber 16 on the > computation node with Intel Xeon Phi Processor 7250 CPU. I have install the > intel complier of 2017 version. > > I have read the help information in the configure file of Amber16. Amber 16 > could be optimized for Intel Xeon Phi Processor by configure it with the > option of -mic_native. > > But when I configure the install configure files as follows: > > ./configure -mic_native intel > > I failed with the Error about NETCDF like this: > > Error: NetCDF C configure returned 77 > > NetCDF configure failed! Check the netcdf_config.log file in > the /home/myxu/soft/amber16/AmberTools/src/ directory. > > The netcdf_config.log is as shown in follows: > > configure: netCDF 4.3.0 > > checking build system type... x86_64-unknown-linux-gnu > > checking host system type... x86_64-k1om-linux-gnu > > checking target system type... x86_64-k1om-linux-gnu > > checking for a BSD-compatible install... /usr/bin/install -c > > checking whether build environment is sane... yes > > checking for x86_64-k1om-linux-strip... no > > checking for strip... strip > > configure: WARNING: using cross tools not prefixed with host > triplet > > checking for a thread-safe mkdir -p... /usr/bin/mkdir -p > > checking for gawk... gawk > > checking whether make sets $(MAKE)... yes > > checking whether make supports nested variables... yes > > configure: checking user options > > checking whether a win32 DLL is desired... no > > checking whether a NCIO_MINBLOCKSIZE was specified... 256 > > checking if fsync support is enabled... no > > checking whether extra valgrind tests should be run... no > > checking whether we should try to build netCDF-4... no > > checking whether reading of HDF4 SD files is to be enabled... no > > checking whether to fetch some sample HDF4 files from Unidata > ftp > site to test HDF4 reading (requires wget)... no > > checking whether parallel I/O for classic and 64-bit offset > files > using parallel-netcdf is to be enabled... no > > checking whether extra example tests should be run... no > > checking whether parallel IO tests should be run... no > > checking whether a default chunk size in bytes was specified... > 4194304 > > checking whether a maximum per-variable cache size for HDF5 was > specified... 67108864 > > checking whether a number of chunks for the default per-variable > cache was specified... 10 > > checking whether a default file cache size for HDF5 was > specified... 4194304 > > checking whether a default file cache maximum number of elements > for HDF5 was specified... 1009 > > checking whether a default cache preemption for HDF5 was > specified... 0.75 > > checking whether netCDF-4 logging is enabled... no > > checking whether cdmremote client is to be built... no > > checking whether DAP client is to be built... no > > checking for style of include used by make... GNU > > checking for x86_64-k1om-linux-gcc... icc -mmic > > checking whether the C compiler works... no > > configure: error: in > `/home/myxu/soft/amber16/AmberTools/src/netcdf-4.3.0': > > configure: error: C compiler cannot create executables > > See `config.log' for more details > > It told me that my C compiler maybe is not suitable, but I have check the > version of my complier like this: > > $ icc -v > > icc version 17.04, gcc version 4.8.5 compatibility > > I don't know how to fix it. Can you help me? > > > Mingyuan > > > 2017.6.4 > > > > > > ------------------------------ > > Message: 9 > Date: Mon, 3 Jul 2017 23:47:42 -0700 > From: Bill Ross <ross.cgl.ucsf.edu> > Subject: Re: [AMBER] Question about installing Amber16 on the intel > Xeon phi computational server > To: amber.ambermd.org > Message-ID: <d037dd8a-348e-48b1-0ebc-d62333be3a8d.cgl.ucsf.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > The directory that is being written in probably has the wrong permissions. > > Bill > > > On 7/3/17 11:44 PM, Mingyuan wrote: > > checking whether the C compiler works... no > > > > configure: error: in > > `/home/myxu/soft/amber16/AmberTools/src/netcdf-4.3.0': > > > > configure: error: C compiler cannot create executables > > > > > ------------------------------ > > Message: 10 > Date: Tue, 4 Jul 2017 12:23:42 +0530 > From: Garima Singh <garimabioinfo.gmail.com> > Subject: [AMBER] Amber md in HPC > To: amber.ambermd.org > Message-ID: > <CAD=mwY1cm71fi_mrFx1p1x15k-nXypkLFywcXur3_FsLYmKXPA.mail. > gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Dear Amber user, > > I am using fewer nodes this time using below > pbs script. Job run and and still > continue but it only give 7 ns /day which is > very slow.How to get fast result > from HPC. Is it slow because of Sander > module.Can i use PMEMD to get fast calculation using HPC. Iour HPC > #!/bin/csh > #PBS -l walltime=48:00:00 > #PBS -N my_job > #PBS -q workq > #PBS -l select=10:ncpus=16:mpiprocs=16 > #PBS -l place=scatter:excl > #PBS -V > > > # Go to the directory from which you submitted the job > cd $PBS_O_WORKDIR > > source /usr/share/Modules/init/csh > setenv MPI_DEBUG "all" > setenv MPI_IB_RAILS "2" > setenv MPI_DSM_DISTRIBUTE "1" > setenv MPI_VERBOSE "1" > setenv MPI_BUFS_THRESHOLD "1" > setenv MPI_BUFS_PER_PROC "1024" > > > source /home/ashoks/amber14/amber14/amber.csh > > module load amber14 > > > module load intel-cluster-studio-2013-sp1 > > cd /home/ashoks/5_garima/pm/pm > mpirun -np 160 sander.MPI -O -i Prod.in -o Prod.out -p cd_cdpm7.prmtop -c > Heat.rst -r prod.rst -x prod.mdcrd -inf p <http://prod.info> > > > *Thank You and Best Wishes* > -- > *Regards* > Garima Singh > AcSIR-PhD Fellow > Biotechnology Division > C/o Dr. Ashok Sharma (Chief Scientist and Head Biotechnology Division) > Central Institute Of Medicinal And Aromatic Plant > CSIR-CIMAP > Lucknow > garimabioinfo.gmail.com > > > > > *INDIA* Please don't print this e-mail unless you really need to. Be Green > ! > > > ------------------------------ > > Message: 11 > Date: Tue, 4 Jul 2017 03:14:21 -0400 > From: Rana Rehan Khalid <rrkhalid.umich.edu> > Subject: Re: [AMBER] xleap editor > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > <CAHy_OfNx7phrwW3dtn2fDKku-ie+3HttUbDb_es+o17-zdLuNg.mail. > gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Is there any setting for num lock key I don't know?? > > On Jul 4, 2017 2:26 AM, "Bill Ross" <ross.cgl.ucsf.edu> wrote: > > > Is your NumLock key set, by any chance? There is some other unexplained > > behavior when that is the case, I believe. > > > > Bill > > > > > > On 7/3/17 9:42 PM, Rana Rehan Khalid wrote: > > > Hi everyone > > > > > > I want to Know how we use xleap unit editor it consist three buttons > like > > > unit, edit and display button when i want to choose any option among > > these > > > button it display the options of that button like unit -----check unit, > > > calculate charge etc. only for the time until i keep pressing the > mouse > > > left button and when i trying to select any of the option the drop down > > > menu of that button disappear when i left the mouse button. kindly tell > > me > > > thanks > > > _______________________________________________ > > > AMBER mailing list > > > AMBER.ambermd.org > > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > ------------------------------ > > Message: 12 > Date: Tue, 4 Jul 2017 07:31:41 +0000 > From: "Elvis Martis" <elvis.martis.bcp.edu.in> > Subject: Re: [AMBER] Amber md in HPC > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > <MAXPR01MB0218D68644A9AE7F596E6260A3D70.MAXPR01MB0218. > INDPRD01.PROD.OUTLOOK.COM> > > Content-Type: text/plain; charset="us-ascii" > > HI, > The speed also depends on the size, i.e. the number atoms in your system. > How many atoms are there in your system? > Secondly, it also depends on what the interconnect device that is used to > connect the various compute nodes. > For InfiniBand switches have low latency time whereas the normal Ethernet > switches have large latency time. > Best Regards > Elvis Martis > Mumbai, INDIA. > > ________________________________________ > From: Garima Singh <garimabioinfo.gmail.com> > Sent: 04 July 2017 12:23:42 > To: amber.ambermd.org > Subject: [AMBER] Amber md in HPC > > Dear Amber user, > > I am using fewer nodes this time using below > pbs script. Job run and and still > continue but it only give 7 ns /day which is > very slow.How to get fast result > from HPC. Is it slow because of Sander > module.Can i use PMEMD to get fast calculation using HPC. Iour HPC > #!/bin/csh > #PBS -l walltime=48:00:00 > #PBS -N my_job > #PBS -q workq > #PBS -l select=10:ncpus=16:mpiprocs=16 > #PBS -l place=scatter:excl > #PBS -V > > > # Go to the directory from which you submitted the job > cd $PBS_O_WORKDIR > > source /usr/share/Modules/init/csh > setenv MPI_DEBUG "all" > setenv MPI_IB_RAILS "2" > setenv MPI_DSM_DISTRIBUTE "1" > setenv MPI_VERBOSE "1" > setenv MPI_BUFS_THRESHOLD "1" > setenv MPI_BUFS_PER_PROC "1024" > > > source /home/ashoks/amber14/amber14/amber.csh > > module load amber14 > > > module load intel-cluster-studio-2013-sp1 > > cd /home/ashoks/5_garima/pm/pm > mpirun -np 160 sander.MPI -O -i Prod.in -o Prod.out -p cd_cdpm7.prmtop -c > Heat.rst -r prod.rst -x prod.mdcrd -inf p <http://prod.info> > > > *Thank You and Best Wishes* > -- > *Regards* > Garima Singh > AcSIR-PhD Fellow > Biotechnology Division > C/o Dr. Ashok Sharma (Chief Scientist and Head Biotechnology Division) > Central Institute Of Medicinal And Aromatic Plant > CSIR-CIMAP > Lucknow > garimabioinfo.gmail.com > > > > > *INDIA* Please don't print this e-mail unless you really need to. Be Green > ! > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > > > > ------------------------------ > > Message: 13 > Date: Tue, 4 Jul 2017 00:33:38 -0700 > From: Bill Ross <ross.cgl.ucsf.edu> > Subject: Re: [AMBER] xleap editor > To: amber.ambermd.org > Message-ID: <aec7ac4e-98b9-6fc3-dba9-67250ce64dd9.cgl.ucsf.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > If it's on, usually a light is on. I don't have one. It just toggles. > > > On 7/4/17 12:14 AM, Rana Rehan Khalid wrote: > > Is there any setting for num lock key I don't know?? > > > > On Jul 4, 2017 2:26 AM, "Bill Ross" <ross.cgl.ucsf.edu> wrote: > > > >> Is your NumLock key set, by any chance? There is some other unexplained > >> behavior when that is the case, I believe. > >> > >> Bill > >> > >> > >> On 7/3/17 9:42 PM, Rana Rehan Khalid wrote: > >>> Hi everyone > >>> > >>> I want to Know how we use xleap unit editor it consist three buttons > like > >>> unit, edit and display button when i want to choose any option among > >> these > >>> button it display the options of that button like unit -----check unit, > >>> calculate charge etc. only for the time until i keep pressing the > mouse > >>> left button and when i trying to select any of the option the drop down > >>> menu of that button disappear when i left the mouse button. kindly tell > >> me > >>> thanks > >>> _______________________________________________ > >>> AMBER mailing list > >>> AMBER.ambermd.org > >>> http://lists.ambermd.org/mailman/listinfo/amber > >> > >> _______________________________________________ > >> AMBER mailing list > >> AMBER.ambermd.org > >> http://lists.ambermd.org/mailman/listinfo/amber > >> > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > ------------------------------ > > Message: 14 > Date: Tue, 4 Jul 2017 07:34:03 +0000 > From: "Elvis Martis" <elvis.martis.bcp.edu.in> > Subject: Re: [AMBER] xleap editor > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > <MAXPR01MB0218ACC0FAB3852A1D6078AFA3D70.MAXPR01MB0218. > INDPRD01.PROD.OUTLOOK.COM> > > Content-Type: text/plain; charset="us-ascii" > > HI, > What Bill meant was just keep your num lock off and all the keys in the > xleap panel will work. > In case you are using a laptop/computer where the keyboard doesn't show a > num lock key, then go to the on-screen keyboard and turn off the num lock > key. > > Best Regards > Elvis Martis > Mumbai, INDIA. > > ________________________________________ > From: Rana Rehan Khalid <rrkhalid.umich.edu> > Sent: 04 July 2017 12:44:21 > To: AMBER Mailing List > Subject: Re: [AMBER] xleap editor > > Is there any setting for num lock key I don't know?? > > On Jul 4, 2017 2:26 AM, "Bill Ross" <ross.cgl.ucsf.edu> wrote: > > > Is your NumLock key set, by any chance? There is some other unexplained > > behavior when that is the case, I believe. > > > > Bill > > > > > > On 7/3/17 9:42 PM, Rana Rehan Khalid wrote: > > > Hi everyone > > > > > > I want to Know how we use xleap unit editor it consist three buttons > like > > > unit, edit and display button when i want to choose any option among > > these > > > button it display the options of that button like unit -----check unit, > > > calculate charge etc. only for the time until i keep pressing the > mouse > > > left button and when i trying to select any of the option the drop down > > > menu of that button disappear when i left the mouse button. kindly tell > > me > > > thanks > > > _______________________________________________ > > > AMBER mailing list > > > AMBER.ambermd.org > > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > > > > ------------------------------ > > Message: 15 > Date: Tue, 4 Jul 2017 00:36:04 -0700 > From: Bill Ross <ross.cgl.ucsf.edu> > Subject: Re: [AMBER] Amber md in HPC > To: amber.ambermd.org > Message-ID: <e81752cd-6c75-c9cf-5472-d80927d12ab7.cgl.ucsf.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > If -np means number of processors, try the 8..32 range perhaps for best > efficiency, test for yourself. > > > On 7/4/17 12:31 AM, Elvis Martis wrote: > > -np 160 > > > > > ------------------------------ > > Message: 16 > Date: Tue, 4 Jul 2017 03:38:57 -0400 > From: Rana Rehan Khalid <rrkhalid.umich.edu> > Subject: Re: [AMBER] xleap editor > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > <CAHy_OfMExdFjhSzVmbag16LxpOEnYRckwncZaCSqw0NVkbF+1A.mail.gmail. > com> > Content-Type: text/plain; charset="UTF-8" > > Thank you Bill and Elvis > > On Jul 4, 2017 3:34 AM, "Elvis Martis" <elvis.martis.bcp.edu.in> wrote: > > > HI, > > What Bill meant was just keep your num lock off and all the keys in the > > xleap panel will work. > > In case you are using a laptop/computer where the keyboard doesn't show a > > num lock key, then go to the on-screen keyboard and turn off the num lock > > key. > > > > Best Regards > > Elvis Martis > > Mumbai, INDIA. > > > > ________________________________________ > > From: Rana Rehan Khalid <rrkhalid.umich.edu> > > Sent: 04 July 2017 12:44:21 > > To: AMBER Mailing List > > Subject: Re: [AMBER] xleap editor > > > > Is there any setting for num lock key I don't know?? > > > > On Jul 4, 2017 2:26 AM, "Bill Ross" <ross.cgl.ucsf.edu> wrote: > > > > > Is your NumLock key set, by any chance? There is some other unexplained > > > behavior when that is the case, I believe. > > > > > > Bill > > > > > > > > > On 7/3/17 9:42 PM, Rana Rehan Khalid wrote: > > > > Hi everyone > > > > > > > > I want to Know how we use xleap unit editor it consist three buttons > > like > > > > unit, edit and display button when i want to choose any option among > > > these > > > > button it display the options of that button like unit -----check > unit, > > > > calculate charge etc. only for the time until i keep pressing the > > mouse > > > > left button and when i trying to select any of the option the drop > down > > > > menu of that button disappear when i left the mouse button. kindly > tell > > > me > > > > thanks > > > > _______________________________________________ > > > > AMBER mailing list > > > > AMBER.ambermd.org > > > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > > > > > _______________________________________________ > > > AMBER mailing list > > > AMBER.ambermd.org > > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > ------------------------------ > > Message: 17 > Date: Tue, 4 Jul 2017 20:34:27 +1000 > From: Daniela Rivas <dani.rivas.r.gmail.com> > Subject: [AMBER] MPI error when trying to run heating > To: amber.ambermd.org > Message-ID: > <CAPen-D5amqGvSckZapf0e=Au0EkrB3nWbrJ1Mvm=jVPA0RBQVQ. > mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Hi all, > > I'm a new amber user and I'm having problems running heating after > minimization. I didn't have any issues when running the minimization with > MPI, but I'm having problems when trying to continue with heating. > > My input file is: > > Membrane-Protein Heating Step 1 > &cntrl > imin = 0, ! No Minimization > ntx = 1, ! Positions read with no initial velocities > irest = 0, ! No Restart > scee = 1.2, ! Scaling factor for 1-4 elesctrostatic interactions > cut = 12, ! Cut-off for vdW and electrostatic interactions > ntc = 2, ! SHAKE on for bond with hydrogen > tol = 0.0005, ! SHAKE tolerance > ntf = 2, ! No force evaluation for bonds with hydrogen > ntt = 3, ! Langevin thermostat > gamma_ln = 5, ! Damping coefficient for Langevin dynamics > ig = -1, ! Random seed for Langevin thermostat > ntp = 0, ! No pressure scaling > ntb = 1, ! Constant volume > ntr = 1, ! Restrain atoms using a harmonic potential > nmropt = 1, ! NMR restraints will be read > nstlim = 5000, ! Number of MD steps > dt = 0.002, ! Timestep in ps > ntpr = 100, ! Print to mdout every ntpr steps > ntwx = 100, ! Write to trajectory file every ntwx steps > ntwr = 1000, ! Write a restart file every ntwr steps > ioutfm = 1, ! Write a binary trajectory > ntxo = 2, ! Write binary restart files > / > &wt > type = 'TEMP0', ! Varies the target temperature TEMP0 > istep1 = 0, ! Initial step > istep2 = 5000, ! Final step > value1 = 0, ! Initial temp0 in K > value2 = 100 ! Final temp0 in K > / > &wt > type = 'END' > / > Hold lipid fixed > 30 ! Force constant > RES 456 1592 ! Lipid residues > END > Protein Backbone C > 30 ! Force constant > FIND > C * * * > SEARCH > RES 1 453 > END > Protein Backbone N > 30 ! Force constant > FIND > N * * * > SEARCH > RES 1 453 > END > Protein Backbone CA > 30 ! Force constant > FIND > CA * * * > SEARCH > RES 1 453 > END > Protein Backbone O > 30 ! Force constant > FIND > O * * * > SEARCH > RES 1 453 > END > Glucose > 30 > RES 454 455 > END > END > > My PBS file is: > > #!/bin/bash > > #PBS -q normalbw > #PBS -P r16 > #PBS -l ncpus=56 > #PBS -l walltime=02:00:00 > #PBS -l mem=8GB > #PBS -l software=amber > #PBS -l other=mpi > #PBS -l wd > > module load openmpi/1.6.3 > module load amber/16-16.05 > > mpirun -np $PBS_NCPUS $AMBERHOME/bin/pmemd.MPI -O -i Heat_01.in -o > Heat_01.out -p GLUT3_InOpen.prmtop -c Min.rst -r Heat_01.rst -ref Min.rst > -x Heat_01.mdcrd > > And the error I get is: > > ------------------------------------------------------- > Primary job terminated normally, but 1 process returned > a non-zero exit code.. Per user-direction, the job has been aborted. > ------------------------------------------------------- > -------------------------------------------------------------------------- > mpirun detected that one or more processes exited with non-zero status, > thus causing > the job to be terminated. The first process to do so was: > > Process name: [[56289,1],0] > Exit code: 19 > > I have been all day trying to figure out what is wrong but I can't find the > error. Any ideas? > > Thanks in advance, > Daniela. > > > ------------------------------ > > Message: 18 > Date: Tue, 4 Jul 2017 03:49:08 -0700 > From: Bill Ross <ross.cgl.ucsf.edu> > Subject: Re: [AMBER] MPI error when trying to run heating > To: amber.ambermd.org > Message-ID: <4c36f9cf-2227-9cbc-5693-5fa05781b46e.cgl.ucsf.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > I suggest trying to run 1000 steps at 10K without restraints, to see if > the problem is with your restraints or your model. > > Also, see the end of your mdout for clues. > > Bill > > On 7/4/17 3:34 AM, Daniela Rivas wrote: > > Hi all, > > > > I'm a new amber user and I'm having problems running heating after > > minimization. I didn't have any issues when running the minimization with > > MPI, but I'm having problems when trying to continue with heating. > > > > My input file is: > > > > Membrane-Protein Heating Step 1 > > &cntrl > > imin = 0, ! No Minimization > > ntx = 1, ! Positions read with no initial velocities > > irest = 0, ! No Restart > > scee = 1.2, ! Scaling factor for 1-4 elesctrostatic > interactions > > cut = 12, ! Cut-off for vdW and electrostatic interactions > > ntc = 2, ! SHAKE on for bond with hydrogen > > tol = 0.0005, ! SHAKE tolerance > > ntf = 2, ! No force evaluation for bonds with hydrogen > > ntt = 3, ! Langevin thermostat > > gamma_ln = 5, ! Damping coefficient for Langevin dynamics > > ig = -1, ! Random seed for Langevin thermostat > > ntp = 0, ! No pressure scaling > > ntb = 1, ! Constant volume > > ntr = 1, ! Restrain atoms using a harmonic potential > > nmropt = 1, ! NMR restraints will be read > > nstlim = 5000, ! Number of MD steps > > dt = 0.002, ! Timestep in ps > > ntpr = 100, ! Print to mdout every ntpr steps > > ntwx = 100, ! Write to trajectory file every ntwx steps > > ntwr = 1000, ! Write a restart file every ntwr steps > > ioutfm = 1, ! Write a binary trajectory > > ntxo = 2, ! Write binary restart files > > / > > &wt > > type = 'TEMP0', ! Varies the target temperature TEMP0 > > istep1 = 0, ! Initial step > > istep2 = 5000, ! Final step > > value1 = 0, ! Initial temp0 in K > > value2 = 100 ! Final temp0 in K > > / > > &wt > > type = 'END' > > / > > Hold lipid fixed > > 30 ! Force constant > > RES 456 1592 ! Lipid residues > > END > > Protein Backbone C > > 30 ! Force constant > > FIND > > C * * * > > SEARCH > > RES 1 453 > > END > > Protein Backbone N > > 30 ! Force constant > > FIND > > N * * * > > SEARCH > > RES 1 453 > > END > > Protein Backbone CA > > 30 ! Force constant > > FIND > > CA * * * > > SEARCH > > RES 1 453 > > END > > Protein Backbone O > > 30 ! Force constant > > FIND > > O * * * > > SEARCH > > RES 1 453 > > END > > Glucose > > 30 > > RES 454 455 > > END > > END > > > > My PBS file is: > > > > #!/bin/bash > > > > #PBS -q normalbw > > #PBS -P r16 > > #PBS -l ncpus=56 > > #PBS -l walltime=02:00:00 > > #PBS -l mem=8GB > > #PBS -l software=amber > > #PBS -l other=mpi > > #PBS -l wd > > > > module load openmpi/1.6.3 > > module load amber/16-16.05 > > > > mpirun -np $PBS_NCPUS $AMBERHOME/bin/pmemd.MPI -O -i Heat_01.in -o > > Heat_01.out -p GLUT3_InOpen.prmtop -c Min.rst -r Heat_01.rst -ref Min.rst > > -x Heat_01.mdcrd > > > > And the error I get is: > > > > ------------------------------------------------------- > > Primary job terminated normally, but 1 process returned > > a non-zero exit code.. Per user-direction, the job has been aborted. > > ------------------------------------------------------- > > ------------------------------------------------------------ > -------------- > > mpirun detected that one or more processes exited with non-zero status, > > thus causing > > the job to be terminated. The first process to do so was: > > > > Process name: [[56289,1],0] > > Exit code: 19 > > > > I have been all day trying to figure out what is wrong but I can't find > the > > error. Any ideas? > > > > Thanks in advance, > > Daniela. > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > ------------------------------ > > Message: 19 > Date: Tue, 4 Jul 2017 11:05:55 +0000 > From: Lizelle Lubbe <LBBLIZ002.myuct.ac.za> > Subject: [AMBER] MCPB.py error step 2 > To: "amber.ambermd.org" <amber.ambermd.org> > Message-ID: > <VI1PR03MB30080F7A05710D21AB9C8A2DB4D70.VI1PR03MB3008. > eurprd03.prod.outlook.com> > > Content-Type: text/plain; charset="iso-8859-1" > > Dear Amber users, > > I am trying to parameterize Zn coordinated to HID, HID, GLU and a water > molecule and have been following the AMBER advanced tutorial 20 on MCPB.py. > > The sidechain model geometry was optimized, force constants calculated for > the large model and the sidechain model fchk file generated. > Next, the Merz-Kollman RESP charge calculation was done followed by the > Gaussian 09 bug fix and espgen in AMBER. > > The tutorial mentions that you should confirm that coordination bonds do > not break. How do I check for this? > > In the final modelling step using the gaussian output I get the following > error: > > [llubbe.login2 04072017_MCPBpycontd]$ MCPB.py -i 03072017_NDOM.in -s 2 > > > > ****************************************************************** > * Welcome to use MCPB.py program * > * Author: Pengfei Li * > * Merz Research Group * > * Michigan State University * > * All Rights Reserved * > ****************************************************************** > > > > The input file you are using is : 03072017_NDOM.in > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > The following is the input variable you have: > The variable original_pdb is : 03072017_NDOM_H_All_renum.pdb > The variable ion_ids is : [9749] > The variable ion_mol2files is : ['ZN_renum.mol2'] > The variable group_name is : NDOM > The variable cut_off is : 2.8 > The variable ionchg_fixation is : 0 > The variable gau_version is : g03 > The variable sqm_opt is : 0 > The variable force_field is : ff14SB > The variable gaff is : 1 > The variable frcmodfs is : [] > The variable naa_mol2files is : ['WAT.mol2'] > The variable water_model is : TIP3P > The variable ion_paraset is : CM (Only for nonbonded model) > The variable ion_info is : [] > ****************************************************************** > * * > *===================Generate the Initial frcmod file=============* > * * > ****************************************************************** > Atoms which has changed the atom types: [5694, 5750, 6151, 9749, 9750] > 361-HID.5694-NE2 : NB --> X1 > 365-HID.5750-NE2 : NB --> X2 > 389-GLU.6151-OE1 : O2 --> X3 > 613-ZN.9749-ZN : ZN --> Z1 > 614-WAT.9750-O : OW --> X4 > ==================Using the Seminario method to solve the problem. > Traceback (most recent call last): > File "/apps/chpc/chem/amber/14/bin/MCPB.py", line 434, in <module> > g0x) > File "/apps/chpc/chem/amber/14/lib/python2.7/site-packages/mcpb/gene_final_frcmod_file.py", > line 306, in gene_by_QM_fitting_sem > 'Int Atom Types') > File "/apps/chpc/chem/amber/14/lib/python2.7/site-packages/pymsmtmol/gauio.py", > line 47, in get_crds_from_fchk > crds.append(float(j)) > ValueError: could not convert string to float: Force > > Any advice on how to solve this would be greatly appreciated! > > Kind regards > > Lizelle Lubbe > > PhD (Medical biochemistry) candidate > Department of Integrative Biomedical Sciences > University of Cape Town > Disclaimer - University of Cape Town This e-mail is subject to UCT > policies and e-mail disclaimer published on our website at > http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from > +27 21 650 9111. If this e-mail is not related to the business of UCT, it > is sent by the sender in an individual capacity. Please report security > incidents or abuse via csirt.uct.ac.za > > > > ------------------------------ > > Message: 20 > Date: Tue, 4 Jul 2017 21:36:45 +1000 > From: Daniela Rivas <dani.rivas.r.gmail.com> > Subject: Re: [AMBER] MPI error when trying to run heating > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: <0EB82529-46BC-465C-9556-5679E3E910C9.gmail.com> > Content-Type: text/plain; charset=us-ascii > > Hi Bill, > > I forgot to mention that I just get the Heat_01.out file. I'm not getting > my .rst or .mdcrd files. In my Heat_01.out file there's no error, but it > ends when finishing reading the input file (Heat_01.in). My guess is that > there's something wrong in my Heat_01.in file. Because it looks like MD > doesn't even start when the error happens. > Also, I don't think my restraints should be any problem. I have ran the > same system with the same conditions in NAMD using AMBER forcefield and I > haven't had any problems. > > Daniela. > > > On 4 Jul 2017, at 8:49 pm, Bill Ross <ross.cgl.ucsf.edu> wrote: > > > > I suggest trying to run 1000 steps at 10K without restraints, to see if > > the problem is with your restraints or your model. > > > > Also, see the end of your mdout for clues. > > > > Bill > > > >> On 7/4/17 3:34 AM, Daniela Rivas wrote: > >> Hi all, > >> > >> I'm a new amber user and I'm having problems running heating after > >> minimization. I didn't have any issues when running the minimization > with > >> MPI, but I'm having problems when trying to continue with heating. > >> > >> My input file is: > >> > >> Membrane-Protein Heating Step 1 > >> &cntrl > >> imin = 0, ! No Minimization > >> ntx = 1, ! Positions read with no initial velocities > >> irest = 0, ! No Restart > >> scee = 1.2, ! Scaling factor for 1-4 elesctrostatic > interactions > >> cut = 12, ! Cut-off for vdW and electrostatic interactions > >> ntc = 2, ! SHAKE on for bond with hydrogen > >> tol = 0.0005, ! SHAKE tolerance > >> ntf = 2, ! No force evaluation for bonds with hydrogen > >> ntt = 3, ! Langevin thermostat > >> gamma_ln = 5, ! Damping coefficient for Langevin dynamics > >> ig = -1, ! Random seed for Langevin thermostat > >> ntp = 0, ! No pressure scaling > >> ntb = 1, ! Constant volume > >> ntr = 1, ! Restrain atoms using a harmonic potential > >> nmropt = 1, ! NMR restraints will be read > >> nstlim = 5000, ! Number of MD steps > >> dt = 0.002, ! Timestep in ps > >> ntpr = 100, ! Print to mdout every ntpr steps > >> ntwx = 100, ! Write to trajectory file every ntwx steps > >> ntwr = 1000, ! Write a restart file every ntwr steps > >> ioutfm = 1, ! Write a binary trajectory > >> ntxo = 2, ! Write binary restart files > >> / > >> &wt > >> type = 'TEMP0', ! Varies the target temperature TEMP0 > >> istep1 = 0, ! Initial step > >> istep2 = 5000, ! Final step > >> value1 = 0, ! Initial temp0 in K > >> value2 = 100 ! Final temp0 in K > >> / > >> &wt > >> type = 'END' > >> / > >> Hold lipid fixed > >> 30 ! Force constant > >> RES 456 1592 ! Lipid residues > >> END > >> Protein Backbone C > >> 30 ! Force constant > >> FIND > >> C * * * > >> SEARCH > >> RES 1 453 > >> END > >> Protein Backbone N > >> 30 ! Force constant > >> FIND > >> N * * * > >> SEARCH > >> RES 1 453 > >> END > >> Protein Backbone CA > >> 30 ! Force constant > >> FIND > >> CA * * * > >> SEARCH > >> RES 1 453 > >> END > >> Protein Backbone O > >> 30 ! Force constant > >> FIND > >> O * * * > >> SEARCH > >> RES 1 453 > >> END > >> Glucose > >> 30 > >> RES 454 455 > >> END > >> END > >> > >> My PBS file is: > >> > >> #!/bin/bash > >> > >> #PBS -q normalbw > >> #PBS -P r16 > >> #PBS -l ncpus=56 > >> #PBS -l walltime=02:00:00 > >> #PBS -l mem=8GB > >> #PBS -l software=amber > >> #PBS -l other=mpi > >> #PBS -l wd > >> > >> module load openmpi/1.6.3 > >> module load amber/16-16.05 > >> > >> mpirun -np $PBS_NCPUS $AMBERHOME/bin/pmemd.MPI -O -i Heat_01.in -o > >> Heat_01.out -p GLUT3_InOpen.prmtop -c Min.rst -r Heat_01.rst -ref > Min.rst > >> -x Heat_01.mdcrd > >> > >> And the error I get is: > >> > >> ------------------------------------------------------- > >> Primary job terminated normally, but 1 process returned > >> a non-zero exit code.. Per user-direction, the job has been aborted. > >> ------------------------------------------------------- > >> ------------------------------------------------------------ > -------------- > >> mpirun detected that one or more processes exited with non-zero status, > >> thus causing > >> the job to be terminated. The first process to do so was: > >> > >> Process name: [[56289,1],0] > >> Exit code: 19 > >> > >> I have been all day trying to figure out what is wrong but I can't find > the > >> error. Any ideas? > >> > >> Thanks in advance, > >> Daniela. > >> _______________________________________________ > >> AMBER mailing list > >> AMBER.ambermd.org > >> http://lists.ambermd.org/mailman/listinfo/amber > > > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > ------------------------------ > > Message: 21 > Date: Tue, 4 Jul 2017 04:57:50 -0700 > From: Bill Ross <ross.cgl.ucsf.edu> > Subject: Re: [AMBER] MPI error when trying to run heating > To: amber.ambermd.org > Message-ID: <9b7bb185-7a94-4c03-27e7-3dcf43674a38.cgl.ucsf.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > Simplification is a strategy available to you, if you want to try it. > > Bill > > > On 7/4/17 4:36 AM, Daniela Rivas wrote: > > Hi Bill, > > > > I forgot to mention that I just get the Heat_01.out file. I'm not > getting my .rst or .mdcrd files. In my Heat_01.out file there's no error, > but it ends when finishing reading the input file (Heat_01.in). My guess is > that there's something wrong in my Heat_01.in file. Because it looks like > MD doesn't even start when the error happens. > > Also, I don't think my restraints should be any problem. I have ran the > same system with the same conditions in NAMD using AMBER forcefield and I > haven't had any problems. > > > > Daniela. > > > >> On 4 Jul 2017, at 8:49 pm, Bill Ross <ross.cgl.ucsf.edu> wrote: > >> > >> I suggest trying to run 1000 steps at 10K without restraints, to see if > >> the problem is with your restraints or your model. > >> > >> Also, see the end of your mdout for clues. > >> > >> Bill > >> > >>> On 7/4/17 3:34 AM, Daniela Rivas wrote: > >>> Hi all, > >>> > >>> I'm a new amber user and I'm having problems running heating after > >>> minimization. I didn't have any issues when running the minimization > with > >>> MPI, but I'm having problems when trying to continue with heating. > >>> > >>> My input file is: > >>> > >>> Membrane-Protein Heating Step 1 > >>> &cntrl > >>> imin = 0, ! No Minimization > >>> ntx = 1, ! Positions read with no initial velocities > >>> irest = 0, ! No Restart > >>> scee = 1.2, ! Scaling factor for 1-4 elesctrostatic > interactions > >>> cut = 12, ! Cut-off for vdW and electrostatic interactions > >>> ntc = 2, ! SHAKE on for bond with hydrogen > >>> tol = 0.0005, ! SHAKE tolerance > >>> ntf = 2, ! No force evaluation for bonds with hydrogen > >>> ntt = 3, ! Langevin thermostat > >>> gamma_ln = 5, ! Damping coefficient for Langevin dynamics > >>> ig = -1, ! Random seed for Langevin thermostat > >>> ntp = 0, ! No pressure scaling > >>> ntb = 1, ! Constant volume > >>> ntr = 1, ! Restrain atoms using a harmonic potential > >>> nmropt = 1, ! NMR restraints will be read > >>> nstlim = 5000, ! Number of MD steps > >>> dt = 0.002, ! Timestep in ps > >>> ntpr = 100, ! Print to mdout every ntpr steps > >>> ntwx = 100, ! Write to trajectory file every ntwx steps > >>> ntwr = 1000, ! Write a restart file every ntwr steps > >>> ioutfm = 1, ! Write a binary trajectory > >>> ntxo = 2, ! Write binary restart files > >>> / > >>> &wt > >>> type = 'TEMP0', ! Varies the target temperature TEMP0 > >>> istep1 = 0, ! Initial step > >>> istep2 = 5000, ! Final step > >>> value1 = 0, ! Initial temp0 in K > >>> value2 = 100 ! Final temp0 in K > >>> / > >>> &wt > >>> type = 'END' > >>> / > >>> Hold lipid fixed > >>> 30 ! Force constant > >>> RES 456 1592 ! Lipid residues > >>> END > >>> Protein Backbone C > >>> 30 ! Force constant > >>> FIND > >>> C * * * > >>> SEARCH > >>> RES 1 453 > >>> END > >>> Protein Backbone N > >>> 30 ! Force constant > >>> FIND > >>> N * * * > >>> SEARCH > >>> RES 1 453 > >>> END > >>> Protein Backbone CA > >>> 30 ! Force constant > >>> FIND > >>> CA * * * > >>> SEARCH > >>> RES 1 453 > >>> END > >>> Protein Backbone O > >>> 30 ! Force constant > >>> FIND > >>> O * * * > >>> SEARCH > >>> RES 1 453 > >>> END > >>> Glucose > >>> 30 > >>> RES 454 455 > >>> END > >>> END > >>> > >>> My PBS file is: > >>> > >>> #!/bin/bash > >>> > >>> #PBS -q normalbw > >>> #PBS -P r16 > >>> #PBS -l ncpus=56 > >>> #PBS -l walltime=02:00:00 > >>> #PBS -l mem=8GB > >>> #PBS -l software=amber > >>> #PBS -l other=mpi > >>> #PBS -l wd > >>> > >>> module load openmpi/1.6.3 > >>> module load amber/16-16.05 > >>> > >>> mpirun -np $PBS_NCPUS $AMBERHOME/bin/pmemd.MPI -O -i Heat_01.in -o > >>> Heat_01.out -p GLUT3_InOpen.prmtop -c Min.rst -r Heat_01.rst -ref > Min.rst > >>> -x Heat_01.mdcrd > >>> > >>> And the error I get is: > >>> > >>> ------------------------------------------------------- > >>> Primary job terminated normally, but 1 process returned > >>> a non-zero exit code.. Per user-direction, the job has been aborted. > >>> ------------------------------------------------------- > >>> ------------------------------------------------------------ > -------------- > >>> mpirun detected that one or more processes exited with non-zero status, > >>> thus causing > >>> the job to be terminated. The first process to do so was: > >>> > >>> Process name: [[56289,1],0] > >>> Exit code: 19 > >>> > >>> I have been all day trying to figure out what is wrong but I can't > find the > >>> error. Any ideas? > >>> > >>> Thanks in advance, > >>> Daniela. > >>> _______________________________________________ > >>> AMBER mailing list > >>> AMBER.ambermd.org > >>> http://lists.ambermd.org/mailman/listinfo/amber > >> > >> _______________________________________________ > >> AMBER mailing list > >> AMBER.ambermd.org > >> http://lists.ambermd.org/mailman/listinfo/amber > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > ------------------------------ > > Message: 22 > Date: Tue, 4 Jul 2017 09:17:33 -0400 > From: Guqin Shi <shi.293.osu.edu> > Subject: [AMBER] Reproduction of MMPBSA Calculations on Processed > Trajectories > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > <CACUf8Hda=uygrKQv0iLaT_dJVF2HHJ17e80Oi5L38scfgM6ozQ. > mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Dear Amber User Community, > > I am recently running MM/PBSA calculations on a huge protein complex. For > one run, I used the raw trajectories with water/ions stripped. For the > other run, I used trajectories processed with center and image in cpptraj > (no water/ions either). Other settings are identical. From MM/PBSA > calculation results, it seems all the MM components are identical (as I > expected); but the PB part are slightly different. like +- 1 unit on a -200 > kcal/mol base. > > I am wondering if this means that center-image post-processing on > trajectories would really affect MM/PBSA calculations (I don't think so > tho...) or this slight difference comes from PBSA calculator precision on > floating numbers...? > > Thank you for your help and time in advanced! I am not sure if I describe > the question clearly, please let me know if more information would help! > > Best, > Guqin > > > -- > Guqin SHI > PhD Candidate in Medicinal Chemistry and Pharmacognosy > College of Pharmacy > The Ohio State University > Columbus, OH, 43210 > https://www.linkedin.com/in/guqin-shi-029bb634 > > > ------------------------------ > > Message: 23 > Date: Tue, 4 Jul 2017 09:57:28 -0400 > From: David Case <david.case.rutgers.edu> > Subject: Re: [AMBER] Amber md in HPC > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: <20170704135728.h2exh3enfbjt3yoc.scarletmail.rutgers.edu> > Content-Type: text/plain; charset=us-ascii > > On Tue, Jul 04, 2017, Garima Singh wrote: > > > > I am using fewer nodes this time using > > below pbs script. Job run and and still continue but it only give 7 > > ns /day which is very slow.How to get fast result from HPC. Is it slow > > because of Sander module.Can i use PMEMD to get fast calculation using > > HPC. > > > mpirun -np 160 sander.MPI .... > > I thought I had replied to this earlier, but maybe the answer got lost... > > 1. 160 is *way* to many threads for sander.MPI. Try something like 8 or > 16. > Experiment with your system to find the best number. > > 2. By all means, run pmemd.MPI: as long as you don't require features > unique > to sander, pmemd will almost always be faster, sometimes by a lot > (especially > with larger numbers of threads.) Again: run experiments to find the best > number of threads. > > ....dac > > > > > ------------------------------ > > Message: 24 > Date: Tue, 4 Jul 2017 10:02:42 -0400 > From: David Case <david.case.rutgers.edu> > Subject: Re: [AMBER] MPI error when trying to run heating > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: <20170704140242.nkuorp7h6m6ohnxn.scarletmail.rutgers.edu> > Content-Type: text/plain; charset=us-ascii > > On Tue, Jul 04, 2017, Daniela Rivas wrote: > > > > I'm a new amber user and I'm having problems running heating after > > minimization. I didn't have any issues when running the minimization with > > MPI, but I'm having problems when trying to continue with heating. > > Bill is correct: divide-and-conquer or simplification is a key to > debugging. > > Start with *short* simulations (nstlim=50) setting ntpr=1. Run in serial > mode. Study the mdout file carefully for anything that looks odd. Since > you > have such complex restraints, try removing them to see if that changes > anything. > > ...good luck....dac > > > > > ------------------------------ > > Message: 25 > Date: Tue, 4 Jul 2017 14:24:10 +0000 > From: N?bia Prates <nnubiaits.hotmail.com> > Subject: Re: [AMBER] How continue a crached minimization step? > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > <BLUPR19MB0001953419FC52E4FE941455BED70.BLUPR19MB0001. > namprd19.prod.outlook.com> > > Content-Type: text/plain; charset="iso-8859-1" > > Bill, > > > Actually I am heaving problems with blackout. I want to continue the > equilibration where it stopped. > > I have attached the .in and mdinfo files. > > > Nubia > > > ________________________________ > De: Bill Ross <ross.cgl.ucsf.edu> > Enviado: segunda-feira, 3 de julho de 2017 17:50 > Para: amber.ambermd.org > Assunto: Re: [AMBER] How continue a crached minimization step? > > It sounds like your machine didn't crash, your simulation did? > > If you are having problems with a simulation getting started, best to > paste the .in file (might as well start with the minimization) into your > mail, along with the part of the output indicating failure. > > Bill > > > On 7/3/17 12:11 PM, N?bia Prates wrote: > > Thank you Elvis and Bill, > > > > > > Now I am heaving the same trouble during the equilibration. > > > > Can you help me with that? > > > > > > Best > > > > N?bia > > > > > > ________________________________ > > De: Bill Ross <ross.cgl.ucsf.edu> > > Enviado: segunda-feira, 3 de julho de 2017 15:21 > > Para: amber.ambermd.org > > Assunto: Re: [AMBER] How continue a crached minimization step? > > > > Usually minimization is not worth running at much length, if it is to > > prepare for dynamics. I would try about 5-30 minutes of wallclock time > > total, so a crash shouldn't matter. Plot the total energy to see what I > > mean. > > > > Bill > > > > On 7/3/17 7:38 AM, N?bia Prates wrote: > >> Hello, > >> > >> I was running a minimization, but it was not completed due to lack of > power. I was wonder if it is possible to continue minimizing where it > stopped or I have to do another? > >> > >> > >> Best > >> > >> N?bia > >> > >> _______________________________________________ > >> AMBER mailing list > >> AMBER.ambermd.org > >> http://lists.ambermd.org/mailman/listinfo/amber > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > lists.ambermd.org > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > lists.ambermd.org > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > lists.ambermd.org > > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > lists.ambermd.org > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > lists.ambermd.org > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > lists.ambermd.org > > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > lists.ambermd.org > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > lists.ambermd.org > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: mdinfo > Type: application/octet-stream > Size: 1422 bytes > Desc: mdinfo > Url : http://lists.ambermd.org/mailman/private/amber/ > attachments/20170704/f89ec726/attachment-0002.obj > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: heat.in > Type: application/octet-stream > Size: 789 bytes > Desc: heat.in > Url : http://lists.ambermd.org/mailman/private/amber/ > attachments/20170704/f89ec726/attachment-0003.obj > > ------------------------------ > > Message: 26 > Date: Tue, 4 Jul 2017 16:25:52 +0200 > From: "Dr. M. Shahid" <mohammad.shahid.gmail.com> > Subject: Re: [AMBER] MCPB.py error step 2 > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > <CABa5kwOzyVNcucBeEn60A6FsBX6V3zf+a1ieSTZcWOevStBaSg.mail. > gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Hi, > > your input file points to the g03 version but you said you used g09? > Also you can try step 2e or 2z if that fits for your Zn system.. > > Best regards, > > -- > Shahid. > > > > On Tue, Jul 4, 2017 at 1:05 PM, Lizelle Lubbe <LBBLIZ002.myuct.ac.za> > wrote: > > > Dear Amber users, > > > > I am trying to parameterize Zn coordinated to HID, HID, GLU and a water > > molecule and have been following the AMBER advanced tutorial 20 on > MCPB.py. > > > > The sidechain model geometry was optimized, force constants calculated > for > > the large model and the sidechain model fchk file generated. > > Next, the Merz-Kollman RESP charge calculation was done followed by the > > Gaussian 09 bug fix and espgen in AMBER. > > > > The tutorial mentions that you should confirm that coordination bonds do > > not break. How do I check for this? > > > > In the final modelling step using the gaussian output I get the following > > error: > > > > [llubbe.login2 04072017_MCPBpycontd]$ MCPB.py -i 03072017_NDOM.in -s 2 > > > > > > > > ****************************************************************** > > * Welcome to use MCPB.py program * > > * Author: Pengfei Li * > > * Merz Research Group * > > * Michigan State University * > > * All Rights Reserved * > > ****************************************************************** > > > > > > > > The input file you are using is : 03072017_NDOM.in > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > > The following is the input variable you have: > > The variable original_pdb is : 03072017_NDOM_H_All_renum.pdb > > The variable ion_ids is : [9749] > > The variable ion_mol2files is : ['ZN_renum.mol2'] > > The variable group_name is : NDOM > > The variable cut_off is : 2.8 > > The variable ionchg_fixation is : 0 > > The variable gau_version is : g03 > > The variable sqm_opt is : 0 > > The variable force_field is : ff14SB > > The variable gaff is : 1 > > The variable frcmodfs is : [] > > The variable naa_mol2files is : ['WAT.mol2'] > > The variable water_model is : TIP3P > > The variable ion_paraset is : CM (Only for nonbonded model) > > The variable ion_info is : [] > > ****************************************************************** > > * * > > *===================Generate the Initial frcmod file=============* > > * * > > ****************************************************************** > > Atoms which has changed the atom types: [5694, 5750, 6151, 9749, 9750] > > 361-HID.5694-NE2 : NB --> X1 > > 365-HID.5750-NE2 : NB --> X2 > > 389-GLU.6151-OE1 : O2 --> X3 > > 613-ZN.9749-ZN : ZN --> Z1 > > 614-WAT.9750-O : OW --> X4 > > ==================Using the Seminario method to solve the problem. > > Traceback (most recent call last): > > File "/apps/chpc/chem/amber/14/bin/MCPB.py", line 434, in <module> > > g0x) > > File "/apps/chpc/chem/amber/14/lib/python2.7/site-packages/mcpb/ > gene_final_frcmod_file.py", > > line 306, in gene_by_QM_fitting_sem > > 'Int Atom Types') > > File "/apps/chpc/chem/amber/14/lib/python2.7/site-packages/ > pymsmtmol/gauio.py", > > line 47, in get_crds_from_fchk > > crds.append(float(j)) > > ValueError: could not convert string to float: Force > > > > Any advice on how to solve this would be greatly appreciated! > > > > Kind regards > > > > Lizelle Lubbe > > > > PhD (Medical biochemistry) candidate > > Department of Integrative Biomedical Sciences > > University of Cape Town > > Disclaimer - University of Cape Town This e-mail is subject to UCT > > policies and e-mail disclaimer published on our website at > > http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from > +27 > > 21 650 9111. If this e-mail is not related to the business of UCT, it is > > sent by the sender in an individual capacity. Please report security > > incidents or abuse via csirt.uct.ac.za > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > ------------------------------ > > Message: 27 > Date: Tue, 4 Jul 2017 22:00:44 +0700 > From: NADIA RAHMAH <nadiiarah.apps.ipb.ac.id> > Subject: [AMBER] Residue number in tleap not appropriate with residue > number in pdb file > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > <CAENwS6LxD-sKT+eoj_AOz5H5WP7YfRmM2-H0x0pp8jw6jehd4A.mail.gmail. > com> > Content-Type: text/plain; charset="UTF-8" > > Hello. I run MD for protein complex docked, in complex pdb file > (preparation result), there are 292 residu number, which 1-291 are protein > (receptor) amino acid residue and residue number 292 is the ligand name > UNL. When I run preparation solvated box and without no box, there are > written like: > there is bond 297 <UNL> <Br> > There is bond 297 <UNL> <H> > > It written UNL in 297 residu. I confuse how Amber read my protein residue > number? How I can see the list of all residue number, I have to know what > is residue number of the ligand, I need to fix it because I want analyst it > with RMSD, MMPBSA, etc. > I hope anybody can help me. Thanks > > > ------------------------------ > > Message: 28 > Date: Tue, 4 Jul 2017 08:01:03 -0700 > From: Bill Ross <ross.cgl.ucsf.edu> > Subject: Re: [AMBER] How continue a crached minimization step? > To: amber.ambermd.org > Message-ID: <8d31effe-fb2f-53c1-0ea0-c966ed67df08.cgl.ucsf.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > Nubia, > > If you have power problems, the solution is to write the restrt file > frequently enough so that a machine crash doesn't hurt too much. If you > didn't write one in your ~22 hours of run time, the best you can do is > be prepared the next time. > > Bill > > > On 7/4/17 7:24 AM, N?bia Prates wrote: > > Bill, > > > > > > Actually I am heaving problems with blackout. I want to continue the > equilibration where it stopped. > > > > I have attached the .in and mdinfo files. > > > > > > Nubia > > > > > > ________________________________ > > De: Bill Ross <ross.cgl.ucsf.edu> > > Enviado: segunda-feira, 3 de julho de 2017 17:50 > > Para: amber.ambermd.org > > Assunto: Re: [AMBER] How continue a crached minimization step? > > > > It sounds like your machine didn't crash, your simulation did? > > > > If you are having problems with a simulation getting started, best to > > paste the .in file (might as well start with the minimization) into your > > mail, along with the part of the output indicating failure. > > > > Bill > > > > > > On 7/3/17 12:11 PM, N?bia Prates wrote: > >> Thank you Elvis and Bill, > >> > >> > >> Now I am heaving the same trouble during the equilibration. > >> > >> Can you help me with that? > >> > >> > >> Best > >> > >> N?bia > >> > >> > >> ________________________________ > >> De: Bill Ross <ross.cgl.ucsf.edu> > >> Enviado: segunda-feira, 3 de julho de 2017 15:21 > >> Para: amber.ambermd.org > >> Assunto: Re: [AMBER] How continue a crached minimization step? > >> > >> Usually minimization is not worth running at much length, if it is to > >> prepare for dynamics. I would try about 5-30 minutes of wallclock time > >> total, so a crash shouldn't matter. Plot the total energy to see what I > >> mean. > >> > >> Bill > >> > >> On 7/3/17 7:38 AM, N?bia Prates wrote: > >>> Hello, > >>> > >>> I was running a minimization, but it was not completed due to lack of > power. I was wonder if it is possible to continue minimizing where it > stopped or I have to do another? > >>> > >>> > >>> Best > >>> > >>> N?bia > >>> > >>> _______________________________________________ > >>> AMBER mailing list > >>> AMBER.ambermd.org > >>> http://lists.ambermd.org/mailman/listinfo/amber > > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > > lists.ambermd.org > > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > > >> AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > > lists.ambermd.org > > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > > >> lists.ambermd.org > >> AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing > List. It is designed to provide a forum for users of the AMBER Molecular > Dynamics and related ... > >> > >> > >> > >> _______________________________________________ > >> AMBER mailing list > >> AMBER.ambermd.org > >> http://lists.ambermd.org/mailman/listinfo/amber > > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > > lists.ambermd.org > > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > > >> AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > > lists.ambermd.org > > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > > >> lists.ambermd.org > >> AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing > List. It is designed to provide a forum for users of the AMBER Molecular > Dynamics and related ... > >> > >> > >> _______________________________________________ > >> AMBER mailing list > >> AMBER.ambermd.org > >> http://lists.ambermd.org/mailman/listinfo/amber > > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > > lists.ambermd.org > > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > > lists.ambermd.org > > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > > > > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > ------------------------------ > > Message: 29 > Date: Tue, 4 Jul 2017 08:49:32 -0700 > From: Bill Ross <ross.cgl.ucsf.edu> > Subject: Re: [AMBER] Residue number in tleap not appropriate with > residue number in pdb file > To: amber.ambermd.org > Message-ID: <57220793-89ad-0f3f-7fdd-72180799e2ab.cgl.ucsf.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > Best to copy/paste actual output. > > Residues get numbered sequentially when leap builds a model, and pdb > residue numbers are lost. > > One way to see the new residue numbers is to savepdb in leap, so you > have a pdb to go from. > > Bill > > > On 7/4/17 8:00 AM, NADIA RAHMAH wrote: > > Hello. I run MD for protein complex docked, in complex pdb file > > (preparation result), there are 292 residu number, which 1-291 are > protein > > (receptor) amino acid residue and residue number 292 is the ligand name > > UNL. When I run preparation solvated box and without no box, there are > > written like: > > there is bond 297 <UNL> <Br> > > There is bond 297 <UNL> <H> > > > > It written UNL in 297 residu. I confuse how Amber read my protein residue > > number? How I can see the list of all residue number, I have to know what > > is residue number of the ligand, I need to fix it because I want analyst > it > > with RMSD, MMPBSA, etc. > > I hope anybody can help me. Thanks > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > ------------------------------ > > Message: 30 > Date: Tue, 4 Jul 2017 16:33:44 +0000 > From: N?bia Prates <nnubiaits.hotmail.com> > Subject: Re: [AMBER] How continue a crached minimization step? > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > <BLUPR19MB0001DFC42402CF32696B265EBED70.BLUPR19MB0001. > namprd19.prod.outlook.com> > > Content-Type: text/plain; charset="iso-8859-1" > > Bill, > > > I am trying to write the rst file, as you suggested, using the command: > > sander -O -i min_rest.in -o rest.out -p .prmtop -c .rst -r rest.rst -ref > .rst > > > But the rst file is not written! What Am I doing wrong? > > > Nubia > > > ________________________________ > De: Bill Ross <ross.cgl.ucsf.edu> > Enviado: ter?a-feira, 4 de julho de 2017 12:01 > Para: amber.ambermd.org > Assunto: Re: [AMBER] How continue a crached minimization step? > > Nubia, > > If you have power problems, the solution is to write the restrt file > frequently enough so that a machine crash doesn't hurt too much. If you > didn't write one in your ~22 hours of run time, the best you can do is > be prepared the next time. > > Bill > > > On 7/4/17 7:24 AM, N?bia Prates wrote: > > Bill, > > > > > > Actually I am heaving problems with blackout. I want to continue the > equilibration where it stopped. > > > > I have attached the .in and mdinfo files. > > > > > > Nubia > > > > > > ________________________________ > > De: Bill Ross <ross.cgl.ucsf.edu> > > Enviado: segunda-feira, 3 de julho de 2017 17:50 > > Para: amber.ambermd.org > > Assunto: Re: [AMBER] How continue a crached minimization step? > > > > It sounds like your machine didn't crash, your simulation did? > > > > If you are having problems with a simulation getting started, best to > > paste the .in file (might as well start with the minimization) into your > > mail, along with the part of the output indicating failure. > > > > Bill > > > > > > On 7/3/17 12:11 PM, N?bia Prates wrote: > >> Thank you Elvis and Bill, > >> > >> > >> Now I am heaving the same trouble during the equilibration. > >> > >> Can you help me with that? > >> > >> > >> Best > >> > >> N?bia > >> > >> > >> ________________________________ > >> De: Bill Ross <ross.cgl.ucsf.edu> > >> Enviado: segunda-feira, 3 de julho de 2017 15:21 > >> Para: amber.ambermd.org > >> Assunto: Re: [AMBER] How continue a crached minimization step? > >> > >> Usually minimization is not worth running at much length, if it is to > >> prepare for dynamics. I would try about 5-30 minutes of wallclock time > >> total, so a crash shouldn't matter. Plot the total energy to see what I > >> mean. > >> > >> Bill > >> > >> On 7/3/17 7:38 AM, N?bia Prates wrote: > >>> Hello, > >>> > >>> I was running a minimization, but it was not completed due to lack of > power. I was wonder if it is possible to continue minimizing where it > stopped or I have to do another? > >>> > >>> > >>> Best > >>> > >>> N?bia > >>> > >>> _______________________________________________ > >>> AMBER mailing list > >>> AMBER.ambermd.org > >>> http://lists.ambermd.org/mailman/listinfo/amber > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > lists.ambermd.org > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > lists.ambermd.org > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > lists.ambermd.org > > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > > >> AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > lists.ambermd.org > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > lists.ambermd.org > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > lists.ambermd.org > > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > > >> lists.ambermd.org > >> AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing > List. It is designed to provide a forum for users of the AMBER Molecular > Dynamics and related ... > >> > >> > >> > >> _______________________________________________ > >> AMBER mailing list > >> AMBER.ambermd.org > >> http://lists.ambermd.org/mailman/listinfo/amber > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > lists.ambermd.org > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > lists.ambermd.org > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > lists.ambermd.org > > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > > >> AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > lists.ambermd.org > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > lists.ambermd.org > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > lists.ambermd.org > > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > > >> lists.ambermd.org > >> AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing > List. It is designed to provide a forum for users of the AMBER Molecular > Dynamics and related ... > >> > >> > >> _______________________________________________ > >> AMBER mailing list > >> AMBER.ambermd.org > >> http://lists.ambermd.org/mailman/listinfo/amber > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > lists.ambermd.org > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > lists.ambermd.org > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > lists.ambermd.org > > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > lists.ambermd.org > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > lists.ambermd.org > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > lists.ambermd.org > > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > > > > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > lists.ambermd.org > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > lists.ambermd.org > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > > ------------------------------ > > Message: 31 > Date: Tue, 4 Jul 2017 09:36:35 -0700 > From: Bill Ross <ross.cgl.ucsf.edu> > Subject: Re: [AMBER] How continue a crached minimization step? > To: amber.ambermd.org > Message-ID: <9fa2cf90-cb1c-6c5e-6557-917410670735.cgl.ucsf.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > There is a mdin variable for setting the frequency of writing it, maybe > ntwr, but check. > > Bill > > > On 7/4/17 9:33 AM, N?bia Prates wrote: > > Bill, > > > > > > I am trying to write the rst file, as you suggested, using the command: > > > > sander -O -i min_rest.in -o rest.out -p .prmtop -c .rst -r rest.rst > -ref .rst > > > > > > But the rst file is not written! What Am I doing wrong? > > > > > > Nubia > > > > > > ________________________________ > > De: Bill Ross <ross.cgl.ucsf.edu> > > Enviado: ter?a-feira, 4 de julho de 2017 12:01 > > Para: amber.ambermd.org > > Assunto: Re: [AMBER] How continue a crached minimization step? > > > > Nubia, > > > > If you have power problems, the solution is to write the restrt file > > frequently enough so that a machine crash doesn't hurt too much. If you > > didn't write one in your ~22 hours of run time, the best you can do is > > be prepared the next time. > > > > Bill > > > > > > On 7/4/17 7:24 AM, N?bia Prates wrote: > >> Bill, > >> > >> > >> Actually I am heaving problems with blackout. I want to continue the > equilibration where it stopped. > >> > >> I have attached the .in and mdinfo files. > >> > >> > >> Nubia > >> > >> > >> ________________________________ > >> De: Bill Ross <ross.cgl.ucsf.edu> > >> Enviado: segunda-feira, 3 de julho de 2017 17:50 > >> Para: amber.ambermd.org > >> Assunto: Re: [AMBER] How continue a crached minimization step? > >> > >> It sounds like your machine didn't crash, your simulation did? > >> > >> If you are having problems with a simulation getting started, best to > >> paste the .in file (might as well start with the minimization) into your > >> mail, along with the part of the output indicating failure. > >> > >> Bill > >> > >> > >> On 7/3/17 12:11 PM, N?bia Prates wrote: > >>> Thank you Elvis and Bill, > >>> > >>> > >>> Now I am heaving the same trouble during the equilibration. > >>> > >>> Can you help me with that? > >>> > >>> > >>> Best > >>> > >>> N?bia > >>> > >>> > >>> ________________________________ > >>> De: Bill Ross <ross.cgl.ucsf.edu> > >>> Enviado: segunda-feira, 3 de julho de 2017 15:21 > >>> Para: amber.ambermd.org > >>> Assunto: Re: [AMBER] How continue a crached minimization step? > >>> > >>> Usually minimization is not worth running at much length, if it is to > >>> prepare for dynamics. I would try about 5-30 minutes of wallclock time > >>> total, so a crash shouldn't matter. Plot the total energy to see what I > >>> mean. > >>> > >>> Bill > >>> > >>> On 7/3/17 7:38 AM, N?bia Prates wrote: > >>>> Hello, > >>>> > >>>> I was running a minimization, but it was not completed due to lack of > power. I was wonder if it is possible to continue minimizing where it > stopped or I have to do another? > >>>> > >>>> > >>>> Best > >>>> > >>>> N?bia > >>>> > >>>> _______________________________________________ > >>>> AMBER mailing list > >>>> AMBER.ambermd.org > >>>> http://lists.ambermd.org/mailman/listinfo/amber > > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > > lists.ambermd.org > > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > > >> AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > > lists.ambermd.org > > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > > >> lists.ambermd.org > >> AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing > List. It is designed to provide a forum for users of the AMBER Molecular > Dynamics and related ... > >> > >> > >>> AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > > lists.ambermd.org > > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > > >> AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > > lists.ambermd.org > > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > > >> lists.ambermd.org > >> AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing > List. It is designed to provide a forum for users of the AMBER Molecular > Dynamics and related ... > >> > >> > >>> lists.ambermd.org > >>> AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing > List. It is designed to provide a forum for users of the AMBER Molecular > Dynamics and related ... > >>> > >>> > >>> > >>> _______________________________________________ > >>> AMBER mailing list > >>> AMBER.ambermd.org > >>> http://lists.ambermd.org/mailman/listinfo/amber > > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > > lists.ambermd.org > > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > > >> AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > > lists.ambermd.org > > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > > >> lists.ambermd.org > >> AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing > List. It is designed to provide a forum for users of the AMBER Molecular > Dynamics and related ... > >> > >> > >>> AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > > lists.ambermd.org > > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > > >> AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > > lists.ambermd.org > > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > > >> lists.ambermd.org > >> AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing > List. It is designed to provide a forum for users of the AMBER Molecular > Dynamics and related ... > >> > >> > >>> lists.ambermd.org > >>> AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing > List. It is designed to provide a forum for users of the AMBER Molecular > Dynamics and related ... > >>> > >>> > >>> _______________________________________________ > >>> AMBER mailing list > >>> AMBER.ambermd.org > >>> http://lists.ambermd.org/mailman/listinfo/amber > > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > > lists.ambermd.org > > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > > >> AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > > lists.ambermd.org > > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > > >> lists.ambermd.org > >> AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing > List. It is designed to provide a forum for users of the AMBER Molecular > Dynamics and related ... > >> > >> > >> > >> _______________________________________________ > >> AMBER mailing list > >> AMBER.ambermd.org > >> http://lists.ambermd.org/mailman/listinfo/amber > > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > > lists.ambermd.org > > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > > >> AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > > lists.ambermd.org > > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > > >> lists.ambermd.org > >> AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing > List. It is designed to provide a forum for users of the AMBER Molecular > Dynamics and related ... > >> > >> > >> > >> > >> _______________________________________________ > >> AMBER mailing list > >> AMBER.ambermd.org > >> http://lists.ambermd.org/mailman/listinfo/amber > > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > > lists.ambermd.org > > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > AMBER -- AMBER Mailing List<http://lists.ambermd.org/ > mailman/listinfo/amber> > > lists.ambermd.org > > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. > It is designed to provide a forum for users of the AMBER Molecular Dynamics > and related ... > > > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > > > ------------------------------ > > Message: 32 > Date: Tue, 4 Jul 2017 13:23:42 -0400 > From: Rana Rehan Khalid <rrkhalid.umich.edu> > Subject: [AMBER] RED ESP not working in these days > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > <CAHy_OfM9GFQxACJAOLw3R7nWFfffhRPnXkkgesGvdR025HT94Q.mail.gmail. > com> > Content-Type: text/plain; charset="UTF-8" > > HI everyone is there any other RED type server which can calculates charges > kindly tell me thanks. > > > ------------------------------ > > Message: 33 > Date: Tue, 4 Jul 2017 13:56:19 -0400 > From: David Cerutti <dscerutti.gmail.com> > Subject: Re: [AMBER] RED ESP not working in these days > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > <CAEmzWj3-bzTDWLaC5TEG=hA7XdHHfs0HhuvD9osExzdizw0GDw.mail. > gmail.com> > Content-Type: text/plain; charset="UTF-8" > > The mdgx program in amber can do it for you. Still need to get the formal > tutorial up on the live website, but: > > http://casegroup.rutgers.edu/~cerutti/amber_web/tutorials/ > advanced/tutorial28/index.php > > The techniques can also be applied to generate straight REsP-like charges > (I say REsP-like because the restraints are harmonic, not hyperbolic, but > the output is hardly different as long as you have a decent amount of > fitting data). > > Dave > > > > On Tue, Jul 4, 2017 at 1:23 PM, Rana Rehan Khalid <rrkhalid.umich.edu> > wrote: > > > HI everyone is there any other RED type server which can calculates > charges > > kindly tell me thanks. > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > ------------------------------ > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > > > End of AMBER Digest, Vol 1985, Issue 1 > ************************************** > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Fri Jul 07 2017 - 04:30:03 PDT