[gmx-users] Pre-equilibrated CHARMM lipid bilayers

[pcl]

Well what works for me is I convert cgenff and merge it with charmm36 (you only have to do this once per cgenff version), then I have paramchem generate cgenff charges for the ligand. Then I convert the output of paramchem (charges) to .rtp format. I also have to create .hdb entries. Paramchem may also generate additional cgenff atom interactions (dihedrals or impropers) that may not exist by default, I usually convert and add those to forcefield's .itp files. Then pdb2gmx will work on the ligand pdb.
________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of James Starlight [jmsstarlight at gmail.com]
Sent: Thursday, December 20, 2012 12:48 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Pre-equilibrated CHARMM lipid bilayers

Peter,


so as I understood after the integration of the CGenFF params into the
charm36 rtp ligand ( in complex with the protein) might be
parametrized just by pdb2gmx. Does this correct ?


James

2012/12/20 Peter C. Lai <pcl at uab.edu>:
> I am not 100% sure how the differences in c36 will affect the parameters you
> get from SwissParam.
>
> Personally I prefer to use ParamChem (CHARMM's version of Swissprot) to
> give me ligand parameters using CGenFF atomtypes, since I have CGenFF
> merged into my Charmm36 forcefield in gromacs.
>
>
> On 2012-12-19 10:37:40AM +0300, James Starlight wrote:
>> Peter, many thanks!
>>
>>
>> Could you tell me is there any differences in atom types between
>> charmm27 and charmm36 ff? I'd like to simulate receptor-ligand complex
>> in that bilayer where ligand molecule would be parametrized by
>> Swiss-param ( make topology for the ligands in charmm27 ff). So
>> because receptor and bilayer will be parametrized in charmm36 I'm not
>> sure about proper working of Swiss's topology with that complex.
>>
>> James
>>
>> 2012/12/19 Peter C. Lai <pcl at uab.edu>:
>> > http://cesium.hyperfine.info/~peter/gromacs/popc36/
>> > has a fully gromacs compatible charmm36 238 POPC bilayer with 21524 waters
>> >
>> > On 2012-12-18 09:07:22PM -0800, James Starlight wrote:
>> >> Justin, thanks again.
>> >>
>> >> As I understood gromacs already had had parameters for charmm lipid so
>> >> the main approach is to do ITP file for 1 lipid by means of pdb2gmx
>> >> isnt it?
>> >>
>> >> By the way is there any way to convert PSF or CRD file to PDB?
>> >>
>> >> I've found suitable bilayer for my simulation but it lack such coordinates.
>> >> POPE Bilayer (310.15K, A=65.2 Â/lipid, 10ns, 340 lipids, noLRCs):
>> >> CHARMM PSF, X-Plor/NAMD PSF, and CHARMM CRD
>> >>
>> >> James
>> >>
>> >> 2012/12/18, Justin Lemkul <jalemkul at vt.edu>:
>> >> >
>> >> >
>> >> > On 12/18/12 2:02 PM, James Starlight wrote:
>> >> >> Dear Gromacs Users!
>> >> >>
>> >> >> I'm looking for 150-200 lipid bilayer ( POPC or POPE) parametrized in
>> >> >> charmm27 or charmm36 force field and pre-equilibrated in NPT
>> >> >> conditions. I'll bevery thankfull to anybody who provide me with the
>> >> >> coordinates as well as itp file for such bilayer.
>> >> >>
>> >> >
>> >> > http://terpconnect.umd.edu/~jbklauda/research/download.html
>> >> >
>> >> > Google is your friend.  There are plenty more places to look.  A search for
>> >> >
>> >> > "POPC CHARMM membrane coordinates" (without the quotes) does the trick.
>> >> >
>> >> > -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
>> >> >
>> >> > ========================================
>> >> > --
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