Re: [AMBER] AMBER Digest, Vol 1985, Issue 1

From: Garima Singh <garimabioinfo.gmail.com>
Date: Fri, 7 Jul 2017 16:53:24 +0530

  Thank you Elvis,Bill and David
                    As per your suggestion i am using 2 nodes 32
processor this time and got 17 ns/day .Which is good as comparison to
previous 7 ns/day. But there is problem my HPC support team could not
increase wall time . I want to run my MD for 50 ns so my job will
terminate after 48 hours which is max wall time set by HPC team. So i want
to know that how to restart job in HPC after termination what kind of
change done in my pbs script?


*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 !
On Wed, Jul 5, 2017 at 12:30 AM, <amber-request.ambermd.org> wrote:
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>
> 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
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> ------------------------------
>
> 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
> >
> > _______________________________________________
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> > 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
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> >
> >> AMBER -- AMBER Mailing List<http://lists.ambermd.org/
> mailman/listinfo/amber>
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> It is designed to provide a forum for users of the AMBER Molecular Dynamics
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> >> 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 ...
> >>
> >>
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> >> AMBER mailing list
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> mailman/listinfo/amber>
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> It is designed to provide a forum for users of the AMBER Molecular Dynamics
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> 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
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>
>
> ------------------------------
>
> 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
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> 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>
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> It is designed to provide a forum for users of the AMBER Molecular Dynamics
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> > 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>
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> It is designed to provide a forum for users of the AMBER Molecular Dynamics
> and related ...
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>
> > AMBER -- AMBER Mailing List<http://lists.ambermd.org/
> mailman/listinfo/amber>
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> It is designed to provide a forum for users of the AMBER Molecular Dynamics
> and related ...
> >
> >
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> >> 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 ...
> >>
> >>
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> 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
> >>>>
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> ------------------------------
>
> 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.
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>
> 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.
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>
> 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.
> > _______________________________________________
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> >
>
>
> ------------------------------
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> End of AMBER Digest, Vol 1985, Issue 1
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