[gmx-users] Charmm to gromacs conversion for lipids
venkat4bt at gmail.com
Wed Nov 5 13:04:03 CET 2014
Thank you Joao for the quick reply. My system has single lipid molecule and
I have pre- calculated charge information for every atom in the lipid. I
have edited charges on individual atoms apart from atom types.
By the way, Previous studies have reported a topology for same lipid but in
NAMD convention. Is there any other tool to convert NAMD to GROMACS
On Wed, Nov 5, 2014 at 3:58 PM, João Martins <joaomartins139 at gmail.com>
> 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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With Best Wishes
Venkat Reddy Chirasani
Laboratory of Computational Biophysics
Department of Biotechnology
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