[gmx-users] How to create a new lipid molecule topology if I have .pdb file for a molecule?

Justin Lemkul jalemkul at vt.edu
Sun May 25 16:37:42 CEST 2014

On 5/24/14, 5:26 PM, Todor Antonijevic wrote:
> Hi,
> I am relatively new user of Gromacs and I struggle for last few weeks to
> create a topology file for a new lipid molecule. I would appreciate any
> help on this matter. In more detail, how one creates a topology file for
> Charmm36, slipid, GAFF and Berger force field just knowing .pdb file for
> that molecule, and is there any useful tutorial or paper that discuss this
> matter?

The primary literature references for those force fields should describe the 
protocol for deriving compatible parameters and validating them.



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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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