[gmx-users] Lipid topologies, carving, etc

[Alex Smolyanitsky]

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.

Thanks,

Alex


On Thu, May 6, 2010 at 1:44 AM, Kukol, Andreas <a.kukol at herts.ac.uk> wrote:

> Alex,
>
> 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.
>
> Andreas
>
>
> > -----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
> >
> >
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100506/959f2f40/attachment.html>