[gmx-users] Lipid topologies, carving, etc
asmolya1 at asu.edu
Thu May 6 20:02:38 CEST 2010
I see. Well, maybe doing the old school manual carving isn't a bad idea,
after all. I still think your script is extremely useful, will definitely
write to you if I need it.
On Thu, May 6, 2010 at 1:44 AM, Kukol, Andreas <a.kukol at herts.ac.uk> wrote:
> 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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