[gmx-users] Lipid topologies, carving, etc

Kukol, Andreas a.kukol at herts.ac.uk
Thu May 6 09:44:32 CEST 2010


I used the membrane builder and even developed a script to convert that POPC into Gro53a6 - please contact me by personal email, if you want it.

Afterwards I found, that the resulting protein/lipid system contained many overlaps between atoms and removing all the overlaps created a membrane with many holes. So in conclusion using the membrane builder was a waste of time.


> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of Alex Smolyanitsky
> Sent: 06 May 2010 04:58
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Lipid topologies, carving, etc
> Hi everyone,
> I am setting up an ion channel in a lipid, and in the past
> I would manually carve the membrane using something like PyMol.
> This time tried the very nice automatic system builder at
> http://www.charmm-gui.org/?doc=input/membrane and the result is
> beautiful. However, the POPC isn't compatible with what's out there
> for the GROMACS 53a6 forcefield, and DPPC isn't compatible with the
> existing rtp entry in 53a6 (a bunch of wrong atom types).
> Other than doing it manually, is there a quick way to make any of
> the resulting lipid coordinates compatible with GROMACS?
> Also, is there any software other than the inflategro script and
> g_membed that helps automate the protein-lipid assembly?
> Thanks a bunch,
> Alex
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