[gmx-users] Charmm to gromacs conversion for lipids

João Martins joaomartins139 at gmail.com
Wed Nov 5 11:29:03 CET 2014

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
> --
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list