[gmx-users] Building lipid bilayers topology

superpc khipinchua at gmail.com
Fri Oct 11 18:24:35 CEST 2013

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?

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?

Best Regards,
Khi Pin

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