Hello Ross,
Thanks for your reply.
I will run the tests and get back with all the log files.
Regards
Elvis Martis
Bombay College of Pharmacy.
> On 24-May-2016, at 00:30, amber-request.ambermd.org wrote:
>
> Send AMBER mailing list submissions to
> amber.ambermd.org
>
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> or, via email, send a message with subject or body 'help' to
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> When replying, please edit your Subject line so it is more specific
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>
> 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 --------------
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>
> ------------------------------
>
> 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
>
>
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>
>
> ------------------------------
>
> 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
> **************************************
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Received on Mon May 23 2016 - 17:30:02 PDT
