[gmx-users] Lipid topologies, carving, etc

Mark Abraham Mark.Abraham at anu.edu.au
Thu May 6 06:21:47 CEST 2010

On 6/05/2010 1:58 PM, Alex Smolyanitsky wrote:
> 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?

Probably. If it's just a matter of changing atom names, or making united 
atoms, or such, then I'd expect a simple perl or sed script will do the 
job nicely. Uploading such scripts to the GROMACS webpage, or simply 
posting them here, in order that others can use them is also a good idea.


> 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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