[gmx-users] Charmm to gromacs conversion for lipids

[João Martins]

The rtp file is used by pdb2gmx for creating GROMACS topology and
coordinate files. Changing it in the lipids.rtp will not do much other than
allow you to generate from a pdb the .gro and .top for that molecule.
Changing atom types is tricky and should be avoided in order to make sure
you're using the cgenff-generated parameters, those atomtypes are connected
to the molecule you submitted and the charmm36.ff used in the conversion.

I'd advise against using cgenff-derived parameters for serious
calculations, the charge penalties are usually pretty high and that means
you won't have a realistic description of your system. However, if you
really want to run a simulation using those parameters, that's perfectly
possible. That command generates a usable topology and coordinate pair, as
well as a parameter file that's loaded in the topology. For all intents and
purposes, using those for a single molecule simulation will work and should
be relatively straightforward. If you want to simulate a multi-molecule
system, you can either manually create a coordinate file modifying the
generated one or, alternatively, generate it using any molecule editing
software, exporting a pdb and using pdb2gmx to generate a
gromacs-compatible coordinate and topology file.



*Joao Martins*

joaomartins139 at gmail.com

On Wed, Nov 5, 2014 at 10:31 AM, Venkat Reddy <venkat4bt at gmail.com> wrote:

> Dear all,
> I have a new lipid molecule and I want to simulate it using charmm36
> forcefield. I have generated .str file using *paramchem* server and then
> using the following command, I got the itp file.
>
> ./cgenff_charmm2gmx.py COL COL.mol2 COL.str charmm36.ff
>
> Is this a reasonable approach for generating gromacs topology for a lipid
> molecule? If I change the atom types in the generated itp file to lipid
> atom types described in lipids.rtp, is it appropriate?
>
> Thank you for your time
>
> --
> With Best Wishes
> Venkat Reddy Chirasani
> PhD student
> Laboratory of Computational Biophysics
> Department of Biotechnology
> IIT Madras
> Chennai
> INDIA-600036
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