[gmx-users] Building lipid bilayers topology
jalemkul at vt.edu
Fri Oct 11 18:41:32 CEST 2013
On 10/11/13 12:24 PM, superpc wrote:
> Hi everyone. I am a relatively new user of GROMACS having recently needed to
> carry out research on proteins aggregation.
> I am currently building a DMPC/DMPG 1:1 membrane by assembling individual
> DMPC and DMPG lipid molecules and then using genconf to generate the amount
> of lipids needed. The DMPC topology was taken from Dr. Tielman website,
> while DMPG was taken from lipidbook.
> Now I am facing issue as to how to I make the topologies for the 2 different
> lipids compatible with each other. The DMPC topology is compatible with
> gromos combined with Berger lipid parameter, while the DMPG was done with
> 54A7. I would like to use 54A7 without Berger lipid parameters, what would
> be the best way to do it? Modifying the residue name? If so, do I only have
> to modify the topology dmpc.itp that comes from Dr. Tielman website, such
> that the residue name follows the 54A7 convention?
Renaming the residue is not the problem; you can call a residue whatever you
like. The problem is in replacing atom types that are part of the parent force
field. The Berger lipids use their own atom types for the lipid atoms; you have
to reassign them with 54A7 atom types. Then you have to decide if the charges
are still adequate after you've messed with the atom types.
> The reason I want to use the lipid without Berger lipid is that there's a
> recent paper http://pubs.acs.org/doi/abs/10.1021/ct300675z
> that suggests that 54A7 is the better united atom FF as compared to the
> other FF commonly used, including the Berger Gromos combination. What is
> your opinion?
Reasonable arguments can be made for a variety of lipid parameter sets. You may
want to consider http://md.chem.rug.nl/cgmartini/index.php/blog/269-jungle2.
Justin A. Lemkul, Ph.D.
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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