On Sat, May 12, 2012 at 9:49 AM, Shima Arasteh <shima_arasteh2...@yahoo.com>wrote:
> Dear gmx users, > > Anybody can guide me to some articles which introduces CHARMM36 > forcefield? I want to study about this forcefield. > > Have a look at this paper: http://pubs.acs.org/doi/abs/10.1021/jp101759q -Anirban Thanks in advance, > Shima > > ------------------------------ > *From:* Anirban <reach.anirban.gh...@gmail.com> > *To:* Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for > GROMACS users <gmx-users@gromacs.org> > *Sent:* Friday, May 11, 2012 9:22 PM > > *Subject:* Re: [gmx-users] Simulation of POPC in water using CHARMM27 > > > > On Fri, May 11, 2012 at 10:08 PM, Shima Arasteh < > shima_arasteh2...@yahoo.com> wrote: > > CHARMM27 or CHARMM36 doesn't make different for me. I just want to get a > good output of simulation. > Before this, Justin also suggested me for CHARMM36. Ok, I will use > CHARMM36. But about the atom types, it's not still clear for me what I need > to do. If I use the CHARMM36, am I supposed to build berger lipids? > > > Actually if you use CHARMM36 FF then no need to use Berger parameters, > since CHARMM36 FF already have the all-atom POPC parameters. But there are > differences among the atom types. So you can use these POPC files (Peter > Lai provided me these files and these were generated for the following > work: (please reference): > Lai, P.C. and Crasto, C.J. > Beyond Modeling: All-Atom Olfactory Receptor Model Simulations > Front. Gene. > Volume 3 Year 2012 Number 61 > DOI: 10.3389/fgene.2012.00061) > > These files worked fine for me (with grompp). Include the popc.itp file in > your .top file. > > -Anirban > > > Thanks, > Shima > > ------------------------------ > *From:* Anirban <reach.anirban.gh...@gmail.com> > *To:* Shima Arasteh <shima_arasteh2...@yahoo.com> > *Sent:* Friday, May 11, 2012 8:58 PM > > *Subject:* Re: [gmx-users] Simulation of POPC in water using CHARMM27 > > > > On Fri, May 11, 2012 at 9:13 PM, Shima Arasteh < > shima_arasteh2...@yahoo.com> wrote: > > Dear Anirban, > No, I have not done. Because I didn't know I need Berger lipids for this > simulation. > > > Actually I think the coordinate and topology files from Tieleman's site > are in accordance with the Berger lipid parameters and hence works with the > united-atom gromos FF. You can also get CHARMM27 lipids from > http://terpconnect.umd.edu/~jbklauda/research/download.html here. And the > atom-type errors can be solved if you can build a proper .hdb file with the > proper corrections for the violating atom names. > > -Anirban > > > Thanks for you reply, > Cheers, > Shima > > ------------------------------ > *From:* Anirban <reach.anirban.gh...@gmail.com> > *To:* Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for > GROMACS users <gmx-users@gromacs.org> > *Sent:* Friday, May 11, 2012 8:10 PM > *Subject:* Re: [gmx-users] Simulation of POPC in water using CHARMM27 > > > > On Fri, May 11, 2012 at 7:36 PM, Shima Arasteh < > shima_arasteh2...@yahoo.com> wrote: > > Dear gmx users, > > I'm going to simulate the POPC in water. > I downloaded required files in Tielman site and made the .top file. Then > included the CHARMM27.ff in the .top file. > When I run the grompp I get the fatal error as below: > Atomtype CB not found > > I have done the same with gromos87.ff . But I didn't see any error. > What's the problem? > Anybody may suggest me how to solve this problem? Is this because of the > forcefield? Or something in .top file goes wrong? > > > Have properly edited the CHARMM27 bonded and nonbonded .itp files to > include the Berger lipid parameters and have you included the POPC > topology? You can follow this tutorial to get an idea: > > https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial > > -Anirban > > > Thanks, > Shima > > -- > 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 > > > > > > > > > > >
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