[gmx-users] Lipid topologies, carving, etc

Alex Smolyanitsky asmolya1 at asu.edu
Thu May 6 05:58:16 CEST 2010

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,


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