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-- "Simplicity in life allows you to focus on what's important" On 24 May 2016 at 00:30, <amber-request.ambermd.org> wrote: > Send AMBER mailing list submissions to > amber.ambermd.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.ambermd.org/mailman/listinfo/amber > or, via email, send a message with subject or body 'help' to > amber-request.ambermd.org > > You can reach the person managing the list at > amber-owner.ambermd.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of AMBER digest..." > > > AMBER Mailing List Digest > > Today's Topics: > > 1. Re: QM/MM Interface (Nisler, Collin R.) > 2. optimised corrections to ff03 (Neha Gandhi) > 3. Re: optimised corrections to ff03 (David Cerutti) > 4. Re: QM/MM Interface (Nisler, Collin R.) > 5. nativecontacts (Neha Gandhi) > 6. Re: obtain or build parameters for non-natural residues > (Karl Kirschner) > 7. Re: nativecontacts (Abelak, Kavin) > 8. CUDA MPI issues (Biplab Ghosh) > 9. Re: CUDA MPI issues (Bill Ross) > 10. Re: MMPBSA.py issue with complex prmtop file (Jason Swails) > 11. Re: MMPBSA- topology files preparation (Jason Swails) > 12. Re: CUDA MPI issues (Jason Swails) > 13. Re: obtain or build parameters for non-natural residues > (David Cerutti) > 14. Re: Problems with GTX titan-X GPU (Ross Walker) > 15. Re: CUDA MPI issues (Ross Walker) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 22 May 2016 23:46:39 +0000 > From: "Nisler, Collin R." <nisler.1.buckeyemail.osu.edu> > Subject: Re: [AMBER] QM/MM Interface > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > < > BN1PR01MB3119DC827CE63D82B131BE9984D0.BN1PR01MB311.prod.exchangelabs.com> > > Content-Type: text/plain; charset="us-ascii" > > When I let Orca finish, I do get a .engrad file that is not empty, and > orca terminates normally. I tried using your files, and I end up getting > the same result as before, an empty .engrad file. When I try to run amber > on the command line, I get the attached error. Could this be relevant at > all? > > ________________________________________ > From: Stanislav Simko <s.simko.uu.nl> > Sent: Sunday, May 22, 2016 4:31:58 AM > To: AMBER Mailing List > Subject: Re: [AMBER] QM/MM Interface > > try to let finish the orca calculation - it shouldn't take very long > (depending on your QM region) to see if you obtain nonzero .engrad > file. This is critical part since Amber can not continue without this > file and it seems to me that there's smth wrong with orca calculation > since the file is created (i.e. orca most probably ran but crashed) but > it's empty. If that tells you nothing then try to run the attached > calculation (you need to prepare .prmtop file yourself though, it's too > big to attach) - i just tested it and it should run fine - the tpl file > is prepared from your .inp (i also attach you the submit script for SGE > batch). > best > stano > -- > > Stanislav Simko. > PhD applicant > Inorganic Chemistry and Catalysis > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: Capture.PNG > Type: image/png > Size: 12344 bytes > Desc: Capture.PNG > Url : > http://lists.ambermd.org/mailman/private/amber/attachments/20160522/73beba3c/attachment-0001.png > > ------------------------------ > > Message: 2 > Date: Mon, 23 May 2016 11:09:04 +1000 > From: Neha Gandhi <n.gandhiau.gmail.com> > Subject: [AMBER] optimised corrections to ff03 > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > < > CA+Hq8HzHqNkxPZsH7AiOe2WUPOUDeDdkh4DpOG0wntuG5jODfw.mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi List, > > I was reading papers on ff03* and ff03*. These force fields are available > for download for gromacs package, however I would like to run it in amber. > I would l like to know which files are required to be modified in amber to > include a cosine correction to ? . i.e. *k*? (kcal/mol) > > and ?? (deg) > > > > Many thanks, > Neha > > - > Regards, > Dr. Neha S. Gandhi, > Vice Chancellor's Research Fellow, > Queensland University of Technology, > 2 George Street, Brisbane, QLD 4000 > Australia > LinkedIn > Research Gate > > > ------------------------------ > > Message: 3 > Date: Sun, 22 May 2016 22:21:07 -0400 > From: David Cerutti <dscerutti.gmail.com> > Subject: Re: [AMBER] optimised corrections to ff03 > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > < > CAEmzWj0N-djoUrFQEZj+WS2dZ_U0iESe7BL0DCSRmu-qMXJusQ.mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi Neha, > > It seems that the folder ${AMBERHOME}/dat/leap/parm/ is the place to > start. In it you'll find frcmod.ff03, which contains Yong's dihedral > parameters. However, that's only one of at least two files you'd need, and > the only other one that I see in there is frcmod.ff03ua. You'll also need > all_amino03.lib for the charges and atom types, in > ${AMBERHOME}/dat/leap/lib/, but the most important file is a leaprc, such > as "leaprc.ff03." That leaprc file is in ${AMBERHOME}/dat/leap/cmd/oldff/, > which indicates that ff03 is no longer in active development, but there's > nothing wrong with using it. If you need to write a frcmod from scratch, > the format of those things can be found at > > http://ambermd.org/formats.html#frcmod > > My advice would be to get in touch with the writers of ff03*, and get a > hold of some structures that you can take single point energies of (use the > simplest energy minimization file with one step, run sander, and compare > the results to the benchmark values the ff03* guys can hopefully provide). > This will be an important step to verifying that you have the correct > parameters, since it looks like you'll need to piece together the ff mod > yourself. > > After you get that, your goal is to make a leaprc.ff03* file in the form of > leaprc.ff03. Critical elements of that file are references to the > appropriate sub-files (all_amino03.lib, frcmod.ff03*) and a proper listing > of the relevant atom types (you can check some of the current protein force > fields, but notice how there is a divergence of atom types--check to make > sure that you know what everything in ff03* is called). Once you've got > frcmod.ff03* and leaprc.ff03* (perhaps call it leaprc.protein.ff03* to > stick with the new conventions), feel free to contribute--we should keep up > with the various mods. > > Dave > > > On Sun, May 22, 2016 at 9:09 PM, Neha Gandhi <n.gandhiau.gmail.com> wrote: > > > Hi List, > > > > I was reading papers on ff03* and ff03*. These force fields are available > > for download for gromacs package, however I would like to run it in > amber. > > I would l like to know which files are required to be modified in amber > to > > include a cosine correction to ? . i.e. *k*? (kcal/mol) > > > > and ?? (deg) > > > > > > > > Many thanks, > > Neha > > > > - > > Regards, > > Dr. Neha S. Gandhi, > > Vice Chancellor's Research Fellow, > > Queensland University of Technology, > > 2 George Street, Brisbane, QLD 4000 > > Australia > > LinkedIn > > Research Gate > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > ------------------------------ > > Message: 4 > Date: Mon, 23 May 2016 06:27:13 +0000 > From: "Nisler, Collin R." <nisler.1.buckeyemail.osu.edu> > Subject: Re: [AMBER] QM/MM Interface > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > < > BN1PR01MB3119A6E4830D1CA292AFFC3984E0.BN1PR01MB311.prod.exchangelabs.com> > > Content-Type: text/plain; charset="us-ascii" > > Please disregard my last email, I finally, at long last, discovered the > issue. Your initial suggestion that it might be calling the wrong orca was > in fact correct, the wrong orca was earlier in my path than the orca I > wanted. The solution was to add this line (in csh) in my submission script: > > setenv PATH $HOME/local/src/orca_3.0.1/orca_3_0_1_linux_x86-64:$PATH > > where orca_3_0_1_linux_x86-64 is the directory where orca is located. > Thanks again so much for your help, I very much appreciate the time you > invested. > > Collin > > > > ________________________________________ > From: Stanislav Simko <s.simko.uu.nl> > Sent: Sunday, May 22, 2016 4:31:58 AM > To: AMBER Mailing List > Subject: Re: [AMBER] QM/MM Interface > > try to let finish the orca calculation - it shouldn't take very long > (depending on your QM region) to see if you obtain nonzero .engrad > file. This is critical part since Amber can not continue without this > file and it seems to me that there's smth wrong with orca calculation > since the file is created (i.e. orca most probably ran but crashed) but > it's empty. If that tells you nothing then try to run the attached > calculation (you need to prepare .prmtop file yourself though, it's too > big to attach) - i just tested it and it should run fine - the tpl file > is prepared from your .inp (i also attach you the submit script for SGE > batch). > best > stano > -- > > Stanislav Simko. > PhD applicant > Inorganic Chemistry and Catalysis > > > > ------------------------------ > > Message: 5 > Date: Mon, 23 May 2016 17:25:36 +1000 > From: Neha Gandhi <n.gandhiau.gmail.com> > Subject: [AMBER] nativecontacts > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > <CA+Hq8Hw58W2byokbcpzNAG= > CcgdAbw2NXLEEDfwx6hLR6t1t_g.mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > I have 60000 frames in total and I am using following command to calculate > contacts (AMBER14 and ambertools15). WIth Ambertools16, it prints fraction > as 0 with the same command. > > nativecontacts :LIG !:POP writecontacts contacts.out resout resout.out > distance 10 includesolvent byresidue map mapout resmap.gnu series seriesout > sout.out reference > > For some residues I can contact fraction > 100. Is it really possible.e.g. > output below > > #Res1 #Res2 TotalFrac Contacts > 442 206 582.479 813 > > Am I doing this correctly? > > -- > Regards, > Dr. Neha S. Gandhi, > Vice Chancellor's Research Fellow, > Queensland University of Technology, > 2 George Street, Brisbane, QLD 4000 > Australia > LinkedIn > Research Gate > > > ------------------------------ > > Message: 6 > Date: Mon, 23 May 2016 09:31:24 +0200 > From: Karl Kirschner <k.n.kirschner.gmail.com> > Subject: Re: [AMBER] obtain or build parameters for non-natural > residues > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > <CAF= > D-bzeZQ1Kr4ek2tFBeEgSt5V7y_cLBWisVyPP8s3WzJLOrg.mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hello Aline, > > The model development of nonstandard residues is a difficult thing to do. > The main issues that one has to consider include a) determining partial > atomic charges that are balanced with your desired force field, b) are > there atom types that already exist in desired force field that can be used > to describe your molecule, or will you need to create new atom types c) > choosing the Lennard-Jones parameters for new atom types, d) parameterizing > any missing bond, angle, and torsion parameters using target experimental > and/or quantum data. Amber's antechamber program is a good place to start, > which can provide AM1-BCC charges easily and approximate missing > parameters. However, to truly optimize bonded parameter one needs to use > target experimental and/or QM data, which can be very time consuming since > you might need to generate QM potential energy curves of various internal > coordinates. The R.E.D. server is a good place for determining more robust > charges that are balanced with a given force field. The other thing to > consider is if these nonstandard residues will be used as part of the > primary sequence of a protein, or if they will be used a nonbonded ligands. > In the former case, one needs to make sure the charges and parameters are > balanced with the protein force field. In the later case, one has the > option of using the GAFF force field for modeling the ligand component. > > Bests, > Karl > > On Fri, May 20, 2016 at 9:45 AM, ALINE THOMAS < > aline.thomas.univ-grenoble-alpes.fr> wrote: > > > Dear Amber users and developers > > > > I am looking for .lib or .frcmod files for amber for two non-natural > > residues > > as gamma-carboxylic glutamic acid (GLA) and beta-hydroxy-aspartate > > residues (BHA), > > could not find anything on the archive, or from any website (PTM, NCAA, > > Bryce lab...) > > > > would you have any helping advice for obtaining them > > or for building them de novo ? never done that, > > > > Thank you very much for your help > > > > Aline > > > > > > -- > > Aline Thomas, PhD > > > > D?partement de Pharmacochimie Mol?culaire > > Universit? Joseph Fourier BP53 > > 470, rue de la chimie > > 38041 Grenoble cedex 9 > > T?l : +33 (0) 4.76.63.53.26 > > Fax : +33 (0) 4.76.63.52.98 > > http://dpm.ujf-grenoble.fr/ > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > > -- > Karl. N. Kirschner, Ph.D. > Research Associate > Bonn-Rhein-Sieg University of Applied Sciences > Grantham-Allee 20, 54757 Sankt Augustin, Germany > > > ------------------------------ > > Message: 7 > Date: Mon, 23 May 2016 09:40:02 +0000 > From: "Abelak, Kavin" <kabelak.rvc.ac.uk> > Subject: Re: [AMBER] nativecontacts > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: <0FEECC9A-3BCC-45F4-9C8A-B3619501E733.rvc.ac.uk> > Content-Type: text/plain; charset="us-ascii" > > Hi Neha, > > As I understand it, if there is more than one native contact between > residue pairs (i.e., contacts between more than one atom pair) you will > likely get fractions > 1. See p583 of the AmberTools15 manual. > > HTH, > Kavin > > > > > > > On 23 May 2016, at 08:25, Neha Gandhi <n.gandhiau.gmail.com<mailto: > n.gandhiau.gmail.com>> wrote: > > I have 60000 frames in total and I am using following command to calculate > contacts (AMBER14 and ambertools15). WIth Ambertools16, it prints fraction > as 0 with the same command. > > nativecontacts :LIG !:POP writecontacts contacts.out resout resout.out > distance 10 includesolvent byresidue map mapout resmap.gnu series seriesout > sout.out reference > > For some residues I can contact fraction > 100. Is it really possible.e.g. > output below > > #Res1 #Res2 TotalFrac Contacts > 442 206 582.479 813 > > Am I doing this correctly? > > -- > Regards, > Dr. Neha S. Gandhi, > Vice Chancellor's Research Fellow, > Queensland University of Technology, > 2 George Street, Brisbane, QLD 4000 > Australia > LinkedIn > Research Gate > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org<mailto:AMBER.ambermd.org> > http://lists.ambermd.org/mailman/listinfo/amber > > > [RVC Logo - link to RVC Website]<http://www.rvc.ac.uk> [Twitter icon - > link to RVC (Official) Twitter] <http://twitter.com/RoyalVetCollege> > [Facebook icon - link to RVC (Official) Facebook] < > http://www.facebook.com/theRVC> [YouTube icon - link to RVC YouTube] < > http://www.youtube.com/user/RoyalVetsLondon?feature=mhee> [Pinterest > icon - link to RVC Pinterest] <http://pinterest.com/royalvetcollege/> > [Instagram icon - link to RVC Instagram] < > http://instagram.com/royalvetcollege> > > This message, together with any attachments, is intended for the stated > addressee(s) only and may contain privileged or confidential information. > Any views or opinions presented are solely those of the author and do not > necessarily represent those of the Royal Veterinary College (RVC). If you > are not the intended recipient, please notify the sender and be advised > that you have received this message in error and that any use, > dissemination, forwarding, printing, or copying is strictly prohibited. > Unless stated expressly in this email, this email does not create, form > part of, or vary any contractual or unilateral obligation. Email > communication cannot be guaranteed to be secure or error free as > information could be intercepted, corrupted, amended, lost, destroyed, > incomplete or contain viruses. Therefore, we do not accept liability for > any such matters or their consequences. Communication with us by email will > be taken as acceptance of the risks inherent in doing so. > > > ------------------------------ > > Message: 8 > Date: Mon, 23 May 2016 16:15:08 +0530 > From: Biplab Ghosh <ghosh.biplab.gmail.com> > Subject: [AMBER] CUDA MPI issues > To: amber.ambermd.org > Message-ID: > <CAGsFkLq66CMe8pvKoa45a_o= > sPSP-jrUF0UO22V_RqK2kBK7hw.mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Dear Amber Experts, > > I am trying to run amber14 using parallel GPUs. > I have 2 "GeForce GTX TITAN X" cards installed > in my workstation and having cuda-7.5 libs. > Individual GPUs are performing but when I run > pmemd.cuda.MPI, it gives me the following error: > > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 > > I then referred to the Amber website to check why GPU communication > is failing. I downloaded "check_p2p.tar.bz2" program from the amber site > and getting the following output upon running. > > [biplab.proline check_p2p]$ ./gpuP2PCheck > CUDA_VISIBLE_DEVICES is unset. > CUDA-capable device count: 2 > GPU0 "GeForce GTX TITAN X" > GPU1 "GeForce GTX TITAN X" > > Two way peer access between: > GPU0 and GPU1: NO > > > Can anyone help me on how to configure my system, so that both > GPU can work in parallel. > > Many thanks and regards > > Biplab Ghosh > Bhabha Atomic Research Center, Mumbai > India. > > -- > "Simplicity in life allows you to focus on what's important" > > > ------------------------------ > > Message: 9 > Date: Mon, 23 May 2016 04:01:05 -0700 > From: Bill Ross <ross.cgl.ucsf.edu> > Subject: Re: [AMBER] CUDA MPI issues > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: <911ea656-fa9a-d257-fd17-bb8aba84e37a.cgl.ucsf.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > From "CUDA_VISIBLE_DEVICES is unset" it appears you haven't set an > environment variable that may be needed. > > E.g. > > http://www.acceleware.com/blog/cudavisibledevices-masking-gpus > > Bill > > On 5/23/16 3:45 AM, Biplab Ghosh wrote: > > Dear Amber Experts, > > > > I am trying to run amber14 using parallel GPUs. > > I have 2 "GeForce GTX TITAN X" cards installed > > in my workstation and having cuda-7.5 libs. > > Individual GPUs are performing but when I run > > pmemd.cuda.MPI, it gives me the following error: > > > > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 > > > > I then referred to the Amber website to check why GPU communication > > is failing. I downloaded "check_p2p.tar.bz2" program from the amber site > > and getting the following output upon running. > > > > [biplab.proline check_p2p]$ ./gpuP2PCheck > > CUDA_VISIBLE_DEVICES is unset. > > CUDA-capable device count: 2 > > GPU0 "GeForce GTX TITAN X" > > GPU1 "GeForce GTX TITAN X" > > > > Two way peer access between: > > GPU0 and GPU1: NO > > > > > > Can anyone help me on how to configure my system, so that both > > GPU can work in parallel. > > > > Many thanks and regards > > > > Biplab Ghosh > > Bhabha Atomic Research Center, Mumbai > > India. > > > > -- > > "Simplicity in life allows you to focus on what's important" > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > ------------------------------ > > Message: 10 > Date: Mon, 23 May 2016 08:53:50 -0400 > From: Jason Swails <jason.swails.gmail.com> > Subject: Re: [AMBER] MMPBSA.py issue with complex prmtop file > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > < > CAEk9e3pNpKOxawZm-WWhdQ0waF6dM-8bTg16FFY0mxQzyAzutg.mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > On Fri, May 20, 2016 at 6:23 PM, Kalenkiewicz, Andrew (NIH/NICHD) [F] < > andrew.kalenkiewicz.nih.gov> wrote: > > > Dear Amber Users, > > > > I'm trying to run MMPBSA.py with residue decomposition, but the job keeps > > failing with the following output: > > > > Loading and checking parameter files for compatibility... > > sander found! Using /usr/local/apps/amber/amber14/bin/sander > > cpptraj found! Using /usr/local/apps/amber/amber14/bin/cpptraj > > Preparing trajectories for simulation... > > 1000 frames were processed by cpptraj for use in calculation. > > > > Running calculations on normal system... > > > > Beginning GB calculations with /usr/local/apps/amber/amber14/bin/sander > > calculating complex contribution... > > calculating receptor contribution... > > File "/usr/local/apps/amber/amber14/bin/MMPBSA.py.MPI", line 104, in > > <module> > > app.run_mmpbsa() > > File > > > "/usr/local/apps/amber/amber14/lib/python2.6/site-packages/MMPBSA_mods/main.py", > > line 218, in run_mmpbsa > > self.calc_list.run(rank, self.stdout) > > File > > > "/usr/local/apps/amber/amber14/lib/python2.6/site-packages/MMPBSA_mods/calculation.py", > > line 82, in run > > calc.run(rank, stdout=stdout, stderr=stderr) > > File > > > "/usr/local/apps/amber/amber14/lib/python2.6/site-packages/MMPBSA_mods/calculation.py", > > line 431, in run > > self.prmtop) + '\n\t'.join(error_list) + '\n') > > CalcError: /usr/local/apps/amber/amber14/bin/sander failed with prmtop > > complex.prmtop! > > > > > > Error occured on rank 127. > > Exiting. All files have been retained. > > > -------------------------------------------------------------------------- > > MPI_ABORT was invoked on rank 127 in communicator MPI_COMM_WORLD > > with errorcode 1. > > > > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > > You may or may not see output from other processes, depending on > > exactly when Open MPI kills them. > > > -------------------------------------------------------------------------- > > File "/usr/local/apps/amber/amber14/bin/MMPBSA.py.MPI", line 104, in > > <module> > > app.run_mmpbsa() > > File > > > "/usr/local/apps/amber/amber14/lib/python2.6/site-packages/MMPBSA_mods/main.py", > > line 218, in run_mmpbsa > > self.calc_list.run(rank, self.stdout) > > File > > > "/usr/local/apps/amber/amber14/lib/python2.6/site-packages/MMPBSA_mods/calculation.py", > > line 82, in run > > calc.run(rank, stdout=stdout, stderr=stderr) > > File > > > "/usr/local/apps/amber/amber14/lib/python2.6/site-packages/MMPBSA_mods/calculation.py", > > line 431, in run > > self.prmtop) + '\n\t'.join(error_list) + '\n') > > CalcError: /usr/local/apps/amber/amber14/bin/sander failed with prmtop > > complex.prmtop! > > > > > > Error occured on rank 125. > > Exiting. All files have been retained. > > [cn0935:52965] 1 more process has sent help message help-mpi-api.txt / > > mpi-abort > > [cn0935:52965] Set MCA parameter "orte_base_help_aggregate" to 0 to see > > all help / error messages > > > > My complex, receptor, and ligand files were generated with ante-MMPBSA.py > > and look fine as far as I can tell. I double checked the strip_mask and > > other likely problems. What other reasons could there be for this error > > message? > > > > ?Check the _MMPBSA_complex_gb.mdout.127 file for any error messages that > have been printed (this is where the real error message is contained -- > MMPBSA.py doesn't know what went wrong, it only knows that something did go > wrong). > > That said, 128 a *lot* of threads for an MMPBSA.py job. I would suggest > switching to 1 CPU with only a couple frames to make debugging easier. > > HTH, > Jason > > -- > Jason M. Swails > > > ------------------------------ > > Message: 11 > Date: Mon, 23 May 2016 08:57:44 -0400 > From: Jason Swails <jason.swails.gmail.com> > Subject: Re: [AMBER] MMPBSA- topology files preparation > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > < > CAEk9e3q+0KT7x+89Tboj8mCkhwsCLv3WdCbVuMtfbA96aC7yDQ.mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > On Sat, May 21, 2016 at 10:44 PM, Kat G <katwin86.gmail.com> wrote: > > > Hi all, > > > > I am interested in MMPBSA estimation for the interaction of protein and > > ligand. My system is a homo-dimer, and each monomer interacts with the > same > > ligand at Mg2+ site. By experiments, we know that only in dimer form and > > with the presence of Mg2+ cofactor, ligands can be bound to the dimer > > structure. Then my question is how should I prepare topology files for > > "receptor" and "ligand" in this case for meaningful calculation. > > > > 1. "Ligand" is ligand 1, and "receptor" is a dimer, 2 Mg2+ ions, and the > > other ligand. Then "complex" is the whole system, except WAT and > > counter-ions. > > > > 2. "Ligand" is both similar ligands, and "receptor" is a dimer with Mg2+ > > ions. > > > > 3. "Ligand" is ligand 1, and "receptor" is just one corresponding monomer > > and Mg2+ ion. Then, complex is just only 1 monomer interacting with 1 > > ligand. > > > > Could it be one of these above cases? I think of the first case but still > > not be sure. Could you please give me any suggestion. > > > > ?They are all valid choices depending on what you are trying to learn. > > HTH, > Jason > > -- > Jason M. Swails > > > ------------------------------ > > Message: 12 > Date: Mon, 23 May 2016 09:22:20 -0400 > From: Jason Swails <jason.swails.gmail.com> > Subject: Re: [AMBER] CUDA MPI issues > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > < > CAEk9e3reVJejFUdsDdfnLGTVPDeVCOM1mpBGVMdQfWg_j8cB2g.mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > On Mon, May 23, 2016 at 6:45 AM, Biplab Ghosh <ghosh.biplab.gmail.com> > wrote: > > > Dear Amber Experts, > > > > I am trying to run amber14 using parallel GPUs. > > I have 2 "GeForce GTX TITAN X" cards installed > > in my workstation and having cuda-7.5 libs. > > Individual GPUs are performing but when I run > > pmemd.cuda.MPI, it gives me the following error: > > > > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 > > > > I then referred to the Amber website to check why GPU communication > > is failing. I downloaded "check_p2p.tar.bz2" program from the amber site > > and getting the following output upon running. > > > > [biplab.proline check_p2p]$ ./gpuP2PCheck > > CUDA_VISIBLE_DEVICES is unset. > > CUDA-capable device count: 2 > > GPU0 "GeForce GTX TITAN X" > > GPU1 "GeForce GTX TITAN X" > > > > Two way peer access between: > > GPU0 and GPU1: NO > > > > > > Can anyone help me on how to configure my system, so that both > > GPU can work in parallel. > > > > ?This does not mean that GPU0 and GPU1 cannot work in parallel, it simply > means that they cannot communicate via the P2P (peer-to-peer) protocol. So > they won't be able to work together *efficiently*. This support comes from > the motherboard, and you need to plug the cards into two PCIe slots that > support this communication. Some motherboards don't support this > communication at all, to my knowledge. If that is the case, there is > nothing you can do to fix P2P connectivity in your computer. > > ?For the error message, you should check your output file for possible > errors. And/or run in serial (or on the CPU) if it's still not clear what > the error is. > > HTH, > Jason\ > -- > Jason M. Swails > > > ------------------------------ > > Message: 13 > Date: Mon, 23 May 2016 10:12:23 -0400 > From: David Cerutti <dscerutti.gmail.com> > Subject: Re: [AMBER] obtain or build parameters for non-natural > residues > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > < > CAEmzWj0qzi+FLFN9Ez14GOb1H9haFaoTwvRy322jXGGVw4QXVg.mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi Aline, > > If you want to fight the good fight and make parameters de-novo, I can walk > you through a pipeline for this. It's something I'm (very) actively > developing, but we're just getting ready to submit the manuscript for the > second-generation protein force field. The charges will be relatively > simple to create, and for the cases you've identified I would imagine that > only retyping CB and CG atoms, respectively, would be necessary, which > greatly limits the number of torsion parameters that would need to be > fitted. There are three protein force fields currently distributed with > Amber: ff14SB, ff15ipq, and FB15. The first and third use the Cornell > charges first minted in 1995, which are very much like what you'd get if > you were to use the R.E.D. server that Karl mentioned. The charges on > ff15ipq are of a different breed, using a protocol I developed with some > IBM people in 2010. > > Whichever charge set you use, you'll need some new torsions. I would > recommend you inherit backbone torsions from whatever force field you > choose to model your nonstandard amino acids after, and when you do that > it's also a good idea to inherit the charges on backbone atoms. I would > imagine that R.E.D. server lets you peg charges to pre-defined values, but > if not I know exactly how to do this in my AmberTools program. > > So, the workflow I'd see here is that you pick one of ff14SB (standard > Amber protein model), ff15ipq (hot off the presses, complete rederivation > of charges and bonded parameters with an updated physics model), or fb15 > (ff14SB charges with rederivation of bonded parameters). Then, make your > library files for the amino acids as they will appear in the protein > (main-chain or terminal groups... just need to know about how they connect > to other residues), refit charges appropriate to whichever protein force > field you chose, differentiate the atom types starting at the point along > the side chain that these amino acids become "nonstandard," and finally > make some conformations and do the torsion fitting. > > Dave > > > On Mon, May 23, 2016 at 3:31 AM, Karl Kirschner <k.n.kirschner.gmail.com> > wrote: > > > Hello Aline, > > > > The model development of nonstandard residues is a difficult thing to > do. > > The main issues that one has to consider include a) determining partial > > atomic charges that are balanced with your desired force field, b) are > > there atom types that already exist in desired force field that can be > used > > to describe your molecule, or will you need to create new atom types c) > > choosing the Lennard-Jones parameters for new atom types, d) > parameterizing > > any missing bond, angle, and torsion parameters using target experimental > > and/or quantum data. Amber's antechamber program is a good place to > start, > > which can provide AM1-BCC charges easily and approximate missing > > parameters. However, to truly optimize bonded parameter one needs to use > > target experimental and/or QM data, which can be very time consuming > since > > you might need to generate QM potential energy curves of various internal > > coordinates. The R.E.D. server is a good place for determining more > robust > > charges that are balanced with a given force field. The other thing to > > consider is if these nonstandard residues will be used as part of the > > primary sequence of a protein, or if they will be used a nonbonded > ligands. > > In the former case, one needs to make sure the charges and parameters are > > balanced with the protein force field. In the later case, one has the > > option of using the GAFF force field for modeling the ligand component. > > > > Bests, > > Karl > > > > On Fri, May 20, 2016 at 9:45 AM, ALINE THOMAS < > > aline.thomas.univ-grenoble-alpes.fr> wrote: > > > > > Dear Amber users and developers > > > > > > I am looking for .lib or .frcmod files for amber for two non-natural > > > residues > > > as gamma-carboxylic glutamic acid (GLA) and beta-hydroxy-aspartate > > > residues (BHA), > > > could not find anything on the archive, or from any website (PTM, NCAA, > > > Bryce lab...) > > > > > > would you have any helping advice for obtaining them > > > or for building them de novo ? never done that, > > > > > > Thank you very much for your help > > > > > > Aline > > > > > > > > > -- > > > Aline Thomas, PhD > > > > > > D?partement de Pharmacochimie Mol?culaire > > > Universit? Joseph Fourier BP53 > > > 470, rue de la chimie > > > 38041 Grenoble cedex 9 > > > T?l : +33 (0) 4.76.63.53.26 > > > Fax : +33 (0) 4.76.63.52.98 > > > http://dpm.ujf-grenoble.fr/ > > > > > > _______________________________________________ > > > AMBER mailing list > > > AMBER.ambermd.org > > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > > > > > > > -- > > Karl. N. Kirschner, Ph.D. > > Research Associate > > Bonn-Rhein-Sieg University of Applied Sciences > > Grantham-Allee 20, 54757 Sankt Augustin, Germany > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > ------------------------------ > > Message: 14 > Date: Mon, 23 May 2016 08:35:23 -0700 > From: Ross Walker <ross.rosswalker.co.uk> > Subject: Re: [AMBER] Problems with GTX titan-X GPU > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: <5B329370-200D-401A-B1AF-7952C3619EF1.rosswalker.co.uk> > Content-Type: text/plain; charset=us-ascii > > Hi Elvis, > > Please try running the following validation suite: > > https://dl.dropboxusercontent.com/u/708185/GPU_Validation_Test.tar.gz > > untar it and edit run_test.x and set gpu_count to the number of GPUs in > your system - likely 1 I am guessing. Change test_count to 10 and > run_large_test to true. Then do: > > nohup ./run_test.x >& run_test.log & > > It will take around 24 hours to run - you can check if it is still running > with nvidia-smi. After it is complete please send the contents of the > GPU_0.log, GPU.large_0.log and run_test.log to the list and we should be > able to help you debug things and determine if it is a bad GPU or something > else. > > All the best > Ross > > > On May 21, 2016, at 03:19, Elvis Martis <elvis.martis.bcp.edu.in> wrote: > > > > Hello, > > I have a strange problem running my simulations using Amber14 on GTX > > Titan-X. Jobs run for several minutes and then die without any error > > message, hence I am unable to figure out what is the problem. I keep > > monitoring the GPU temperature while a job is running and it never > crosses > > 82C. > > This GPU card was obtained as gift from NVIDIA as seeding grant. > > Some information on my system. > > Amber version- Amber14 and AmberTools15 <all updates applied> > > CenOS release- centos-release-6-7.el6.centos.12.3.x86_64 > > CUDA version- CUDA-7.5 (Driver version 352.79) <see attachments for > > complete system log generated using "nvidia-smi -q" nvidia.log and > > nvidia-smi.txt> > > CPU- Intel(R) Core(TM) i7-4790 CPU . 3.60GHz <see attached file cpu.log> > > > > Please let me know if any more information is needed to help me solve > this > > problem. > > Thanks in advance for your Help. > > Regards > > > > *Elvis Martis* PhD Student, Bombay College of Pharmacy > > [image: photo] Website: http://www.elvismartis.in > > <http://www.elvismartis.in/> > > Address: Kalina, Santa Cruz [E] > > > > <https://in.linkedin.com/in/elvisadrianmartis> > > > <nvidia-smi.txt><nvidia.log><cpu.log>_______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > ------------------------------ > > Message: 15 > Date: Mon, 23 May 2016 08:47:36 -0700 > From: Ross Walker <ross.rosswalker.co.uk> > Subject: Re: [AMBER] CUDA MPI issues > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: <6A3AD813-8F26-426E-874C-99432938353F.rosswalker.co.uk> > Content-Type: text/plain; charset=us-ascii > > Hi Biplab, > > How are you actually running the calculation across two GPUs? Are you > using mpirun? As in > > mpirun -np 2 $AMBERHOME/bin/pmemd.cuda.MPI -O -i ... > > It's unclear from your description if you are doing this or not. I'd > suggest reading through the instructions on http://ambermd.org/gpus/ to > make sure you are runnings things correctly. If you are then we can do some > further debugging - e.g. take a look in the mdout file etc. - Do the test > cases work in parallel, does CPU parallel work etc? > > With regards to P2P support - this is required if you want to see speedup > across 2 GPUs. Who manufacturers your system? In the first instance you > should go back to them and request details on how to reconfigure the > hardware to support P2P connectivity. If it is a home built system then > please send the motherboard spec (make and model) and we can try and figure > out how the GPUs should be installed to support this. > > All the best > Ross > > > On May 23, 2016, at 03:45, Biplab Ghosh <ghosh.biplab.gmail.com> wrote: > > > > Dear Amber Experts, > > > > I am trying to run amber14 using parallel GPUs. > > I have 2 "GeForce GTX TITAN X" cards installed > > in my workstation and having cuda-7.5 libs. > > Individual GPUs are performing but when I run > > pmemd.cuda.MPI, it gives me the following error: > > > > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 > > > > I then referred to the Amber website to check why GPU communication > > is failing. I downloaded "check_p2p.tar.bz2" program from the amber site > > and getting the following output upon running. > > > > [biplab.proline check_p2p]$ ./gpuP2PCheck > > CUDA_VISIBLE_DEVICES is unset. > > CUDA-capable device count: 2 > > GPU0 "GeForce GTX TITAN X" > > GPU1 "GeForce GTX TITAN X" > > > > Two way peer access between: > > GPU0 and GPU1: NO > > > > > > Can anyone help me on how to configure my system, so that both > > GPU can work in parallel. > > > > Many thanks and regards > > > > Biplab Ghosh > > Bhabha Atomic Research Center, Mumbai > > India. > > > > -- > > "Simplicity in life allows you to focus on what's important" > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > ------------------------------ > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > > > End of AMBER Digest, Vol 1585, Issue 1 > ************************************** >