[gmx-users] Forcefield for Lipids

Justin A. Lemkul jalemkul at vt.edu
Thu Oct 6 13:48:05 CEST 2011

Saumya wrote:
> Hello all,
> I am trying to simulate the DMPC Lipid Bilayer with water molecules. I 
> am using Charmm27 forcefield for that. I obtain the starting structure 
> from Charmm-GUI. The pdb file that I obtain has "DMPC" as the residue 
> name for the lipid molecules. I checked the "lipid.rtp" file in Charmm27 
> and it has DMPC in the list of lipids. But, when I generate the topology 
> using pdb2gmx, it says that it does not recognize the the DMPC residue. 

Please copy and paste the exact error message.

> Therefore, the resulting topology file does not include any information 
> about the lipids and only states the solvent information.
> How can I generate a topology that will include the DMPC lipids too and 
> what residues name is recognized by Gromacs for the DMPC lipid? 

Without seeing the error, it's hard to say.  Also note that pdb2gmx is not 
typically used for many-molecule systems like bilayers.  You'll get a redundant 
topology that is not wrong, but will be very cumbersome to use and understand.

The better approach is to:

1. Isolate a single DMPC lipid from your .pdb file
2. Run pdb2gmx on this single lipid
3. Modify the resulting .top into a .itp file (see 
4. Construct a simple topology, i.e.:

#include "charmm27.ff/forcefield.itp"
#include "dmpc.itp"
#include (water model you need)

[ system ]

[ molecules ]
(fill this in)



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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