[gmx-users] Simulation of POPC in water using CHARMM27

[Anirban]

On Sat, May 12, 2012 at 9:49 AM, Shima Arasteh
<shima_arasteh2001 at 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.ghosh at gmail.com>
> *To:* Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for
> GROMACS users <gmx-users at 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_arasteh2001 at 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.ghosh at gmail.com>
> *To:* Shima Arasteh <shima_arasteh2001 at 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_arasteh2001 at 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.ghosh at gmail.com>
> *To:* Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for
> GROMACS users <gmx-users at 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_arasteh2001 at 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
>
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