[gmx-users] Charmm to gromacs conversion for lipids

Justin Lemkul jalemkul at vt.edu
Wed Nov 5 13:23:05 CET 2014

On 11/5/14 5:28 AM, João Martins wrote:
> 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

In fairness, though, the topology produced by CGenFF tells users what magnitude 
of penalty is considered acceptable and what magnitude requires the user to do a 
bit of work on their own to improve the quality of the topology.  Anyone that 
blindly uses a topology with high penalties...well, the quality of what comes 
out depends on the quality of what goes in :)

CGenFF parameters can be used for "serious calculations," as we do all the time, 
provided the user understands what the limitations are and what additional work 
might be expected.  It's impossible for us to cover all chemical space, so some 
of the analogies assigned by the CGenFF program are inherently poor, but are the 
"best guess" for that particular molecule, within the caveat that we can't do 
everything yet (if ever).


> 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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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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