Thanks Berk, I have found the script, I will try them
Best Stephane ---------------------------------------- Message: 4 Date: Thu, 14 Feb 2013 13:53:56 +0100 From: Berk Hess <g...@hotmail.com> Subject: RE: [gmx-users] Re: GROMOS54A8 parameters in GROMACS format To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <dub124-w200b8c2eb085c78933a9418e...@phx.gbl> Content-Type: text/plain; charset="iso-8859-1" Hi, There are two scripts make_gromos_rtp in the scripts directory which were used to convert Gromos AA topologies to rtp entries. Cheers, Berk ---------------------------------------- > From: stephane.a...@cea.fr > To: gmx-users@gromacs.org > Date: Thu, 14 Feb 2013 11:34:59 +0000 > Subject: [gmx-users] Re: GROMOS54A8 parameters in GROMACS format > > Hello, > > Yeap, I have seen the links on ATB. Indeed, the conversion of the bonded > terms (in this file 54a8.ifp ?) will be not too hard, but it is not the case > for the AA topology where several changes were done. > > So any help will be appreciate.. > > Stephane > > ------------------------------ > > Message: 5 > Date: Thu, 14 Feb 2013 11:18:17 +0100 > From: "lloyd riggs" <lloyd.ri...@gmx.ch> > Subject: Re: [gmx-users] GROMOS54A8 parameters in GROMACS format > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <20130214101817.72...@gmx.net> > Content-Type: text/plain; charset="utf-8" > > Dear Stephane Abel, > > Theres a link I on the gromacs web site to ATB, or you can google it. If it > is not in Gromacs format you can just write a couple 6 liner scripts to > re-format it by parsing into the gromacs format, > > Stephan Watkins > > -------- Original-Nachricht -------- > > Datum: Wed, 13 Feb 2013 21:25:33 +0000 > > Von: ABEL Stephane 175950 <stephane.a...@cea.fr> > > An: "gmx-users@gromacs.org" <gmx-users@gromacs.org> > > Betreff: [gmx-users] GROMOS54A8 parameters in GROMACS format > > > Hello all, > > > > Does somebody know where i can find the latest GROMOS force field (i.e. > > GROMOS54A8) described in [1] in the GROMACS format (gromos54a7.ff) ? > > > > [1] Reif et al. J. Chem. Theory Comput. 2013, 9, 1247???1264 doi: > > http://pubs.acs.org/doi/citedby/10.1021/ct300156h > > > > Thank you > > > > Stephane > > > ------------------------------ > > -- > gmx-users mailing list > gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > End of gmx-users Digest, Vol 106, Issue 73 > ****************************************** > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists ------------------------------ Message: 5 Date: Thu, 14 Feb 2013 08:01:43 -0500 From: Justin Lemkul <jalem...@vt.edu> Subject: Re: [gmx-users] different springs - WHAM To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <511ce037.5020...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 2/13/13 5:23 PM, Steven Neumann wrote: > On Tue, Feb 12, 2013 at 5:01 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >> On 2/12/13 9:57 AM, Steven Neumann wrote: >>> >>> On Tue, Feb 12, 2013 at 2:53 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>>> >>>> >>>> >>>> On 2/12/13 9:40 AM, Steven Neumann wrote: >>>>> >>>>> >>>>> Dear Gmx Users, >>>>> >>>>> I know it is possible to combine windows with different spring >>>>> constants into the one PMF curve using g_wham. >>>>> >>>>> Do I have to somehow tell g_wham that one or two windows have >>>>> different spring constants? >>>>> >>>> >>>> No, they are read from the .tpr files. >>>> >>>> >>>>> For instance - I got the better histogram overlap with lower force >>>>> constant in one window. When I replace this window into the window >>>>> with the sring constant like all windwos (worse overlap) both PMF >>>>> curves differ app. 2kcal/mol which is around 30% of the overall >>>>> deltaG. >>>>> >>>>> Is there any error I should inroduce when one window differ in terms of >>>>> k1? >>>>> >>>> >>>> What does g_wham's error analysis suggest? >>>> >>>> -Justin >>> >>> >>> In both PMF error estimate with bayesian bootstraping is app. 0.2 kcal/mol >>> >> >> Seems like a good result, so what's the problem? >> >> -Justin > > That the better overlap of histograms produce worse deltaG comparing > to experiment. With all the same spring constants I get the > experimental value of deltaG but there is a poor overlap. There must > be (somehow) a correction added to deltaG when introdcuing windows > with different spring constants. > The code and/or g_wham paper should address this. In principle, WHAM can be conducted with any assortment of spring constants you like. If you track down a bug or something, please report it on redmine.gromacs.org. A workaround of course would be to simply add another window (or windows) with the same original force constant that gives adequate sampling. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== ------------------------------ Message: 6 Date: Thu, 14 Feb 2013 08:03:28 -0500 From: Justin Lemkul <jalem...@vt.edu> Subject: Re: [gmx-users] Implicit solvent To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <511ce0a0.8040...@vt.edu> Content-Type: text/plain; charset=UTF-8; format=flowed On 2/14/13 1:01 AM, ?????????????? ???????????????? wrote: > Hi, dear developers! > > I want to ask you abou dynamics in implicit solvent. I have a complex of > animal protein - dimer/trimer. After modeling by homology I have built > another one from the plant organism. Dimer/trimer was constructed with > superposition method. The question is - can I use imlicit solvent model to > optimize and relax this complex? Is it real and where I can find suitable > parameters of mdp? > Infinite cutoffs with a nonperiodic unit cell are generally advisable for running implicit solvent calculations. They don't parallelize well due to a bug that I believe is still being fixed, so you can only run on 1-2 processors in implicit solvent. Performance for large systems actually scales better in explicit solvent, especially if you use GPU acceleration. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== ------------------------------ Message: 7 Date: Thu, 14 Feb 2013 08:04:51 -0500 From: Justin Lemkul <jalem...@vt.edu> Subject: Re: [gmx-users] md with multiple ligands To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <511ce0f3.8000...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 2/14/13 1:20 AM, Ansuman Biswas wrote: > ---------------------------- Original Message ---------------------------- > Subject: Re: gmx-users Digest, Vol 106, Issue 68 > From: ansuman@localhost > Date: Thu, February 14, 2013 10:16 am > To: gmx-users@gromacs.org > -------------------------------------------------------------------------- > > >> >> Message: 8 >> Date: Wed, 13 Feb 2013 08:28:00 -0500 >> From: Justin Lemkul <jalem...@vt.edu> >> Subject: Re: [gmx-users] md with multiple ligands >> To: Discussion list for GROMACS users <gmx-users@gromacs.org> >> Message-ID: <511b94e0.4040...@vt.edu> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> >> >> On 2/13/13 5:24 AM, Ansuman Biswas wrote: >>> >>> Dear gromacs users, >>> >>> I wish to run a protein ligand md in Gromacs 4.5.3 with charmm force >>> field. Its a dimeric protein with a MG ion and 2 ligands bound to two >>> active sites. I wish to run the dimer and there would be 4 ligands. I >>> generated the topology files (.itp) of ligands using SWISSPARAM. Before >>> running the energy minimization I changed the topol.top file accordingly >>> as mentioned in the SWISSPARAM website. I added all the itp files >>> together.But while running GROMPP I got an error message like, >>> >>> >>> WARNING 1 [file ADP.itp, line 24]: >>> Overriding atomtype NPYL >>> >>> >>> WARNING 2 [file ADP.itp, line 25]: >>> Overriding atomtype C5A >>> >>> >>> WARNING 3 [file ADP.itp, line 26]: >>> Overriding atomtype N5B >>> >>> >>> WARNING 4 [file ADP.itp, line 27]: >>> Overriding atomtype C5B >>> >>> >>> WARNING 5 [file ADP.itp, line 28]: >>> Overriding atomtype CB >>> >>> >>> WARNING 6 [file ADP.itp, line 29]: >>> Overriding atomtype NPYD >>> >>> >>> WARNING 7 [file ADP.itp, line 30]: >>> Overriding atomtype PO4 >>> >>> >>> WARNING 8 [file ADP.itp, line 31]: >>> Overriding atomtype O2CM >>> >>> >>> WARNING 9 [file ADP.itp, line 32]: >>> Overriding atomtype OR >>> >>> >>> WARNING 10 [file ADP.itp, line 33]: >>> Overriding atomtype CR >>> >>> >>> WARNING 11 [file ADP.itp, line 34]: >>> Overriding atomtype NC=C >>> >>> >>> WARNING 12 [file ADP.itp, line 35]: >>> Overriding atomtype HCMM >>> >>> >>> WARNING 13 [file ADP.itp, line 36]: >>> Overriding atomtype HNCO >>> >>> >>> WARNING 14 [file ADP.itp, line 37]: >>> Overriding atomtype HOCO >>> >>> >>> WARNING 15 [file ADP.itp, line 38]: >>> Overriding atomtype HOR >>> >>> >>> WARNING 16 [file ADP.itp, line 43]: >>> Overriding atomtype PO4 >>> >>> >>> WARNING 17 [file ADP.itp, line 44]: >>> Overriding atomtype O2CM >>> >>> >>> WARNING 18 [file ADP.itp, line 45]: >>> Overriding atomtype OR >>> >>> >>> WARNING 19 [file ADP.itp, line 46]: >>> Overriding atomtype CR >>> >>> >>> WARNING 20 [file ADP.itp, line 48]: >>> Overriding atomtype HCMM >>> >>> >>> WARNING 21 [file ADP.itp, line 49]: >>> Overriding atomtype HOR >>> >>> >>> WARNING 22 [file ADP.itp, line 50]: >>> Overriding atomtype HOCO >>> >>> >>> WARNING 23 [file ADP.itp, line 52]: >>> Overriding atomtype NC=O >>> >>> >>> WARNING 24 [file ADP.itp, line 53]: >>> Overriding atomtype C=O >>> >>> >>> WARNING 25 [file ADP.itp, line 54]: >>> Overriding atomtype N=C >>> >>> >>> WARNING 26 [file ADP.itp, line 55]: >>> Overriding atomtype C=C >>> >>> >>> WARNING 27 [file ADP.itp, line 56]: >>> Overriding atomtype PO4 >>> >>> >>> WARNING 28 [file ADP.itp, line 57]: >>> Overriding atomtype O2CM >>> >>> >>> WARNING 29 [file ADP.itp, line 58]: >>> Overriding atomtype OR >>> >>> >>> WARNING 30 [file ADP.itp, line 59]: >>> Overriding atomtype CR >>> >>> >>> WARNING 31 [file ADP.itp, line 60]: >>> Overriding atomtype O=C >>> >>> >>> WARNING 32 [file ADP.itp, line 61]: >>> Overriding atomtype HCMM >>> >>> >>> WARNING 33 [file ADP.itp, line 62]: >>> Overriding atomtype HOCO >>> >>> >>> WARNING 34 [file ADP.itp, line 63]: >>> Overriding atomtype HOR >>> >>> >>> WARNING 35 [file ADP.itp, line 64]: >>> Overriding atomtype HOCC >>> >>> Generated 25425 of the 25425 non-bonded parameter combinations >>> Generating 1-4 interactions: fudge = 1 >>> Generated 22285 of the 25425 1-4 parameter combinations >>> >>> ------------------------------------------------------- >>> Program grompp, VERSION 4.5.3 >>> Source code file: toppush.c, line: 1071 >>> >>> Fatal error: >>> Atoms in the .top are not numbered consecutively from 1 (rather, atomnr >>> = >>> 1, while at->nr = 40) >>> >>> I know that the problem is related to the merging of 4 itp files. >>> Please let me how I should do that. >>> >> >> The ligands probably use common atom types and each .itp file likely has >> an >> [atomtypes] directive that introduces these new types. Probably the >> easiest >> thing to do is create a merged [atomtypes] directive that lists all of the >> necessary atom types so you don't list them separately in each file. One >> approach that I have used in the past is to create an .itp file that only >> has >> atom types in it, then call something like: >> >> #include "charmm27.ff/forcefield.itp" >> >> ; only has [atomtypes] >> #include "my_ligand_atomtypes.itp" >> >> ; these don't introduce [atomtypes] any more >> #include "ligand1.itp" >> #include "ligand2.itp" >> >> -Justin > But according to SWISSPARAM website I can only add one ligand.itp file. Just a guess, but it's probably because each ligand.itp file introduces new atom types which give the conflicts above. > So, is it possible to add ligand1 and ligand2 itp files? > Sure, my method should work. Please try it. I have done the exact same thing with Amber topologies from acpype. > Will it be ok if I merge all the ligand pdbs and then get the combined itp > file using that from SWISSPARAM and follow the protocol for one ligand? > Merging the coordinate files will probably not work. If you have multiple molecules, you need multiple topologies. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== ------------------------------ -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! 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