[gmx-users] Fwd: membrane simulations with gromacs

chris.neale at utoronto.ca chris.neale at utoronto.ca
Sat Aug 2 18:34:57 CEST 2008

Dear Landry,

If you didn't find instructions on the mailing list then I suspect  
that you didn't try too many keyword combinations. It's also a good  
idea to peruse the most recent couple of weeks from the archive to  
ensure that the same question was not just answered a couple of days  
ago (it was, by me).

And please keep this on the mailing list. If you wish, you can also  
send me an email to notify me of your recent post to the mailing list.


----- Forwarded message from Landry.CHARLIER at unice.fr -----
     Date: Sat,  2 Aug 2008 16:52:46 +0200
     From: Landry.CHARLIER at unice.fr
Reply-To: Landry.CHARLIER at unice.fr
  Subject: membrane simulations with gromacs
       To: chris.neale at utoronto.ca

Dear Chris Neale
I'm a Ph.D student in computational chemistry and I try to simulate a  
GPCR in a
membrane bilayer of POPC.
Normally, I work with Amber package but Gromacs is more suitable for GPCR
incorporation in a membrane bilayer.
Like POPC parameters aren't in the database of Gromacs, I try to use  
Gromacs on
simple case : the popc128b.pdb of Pr. Tieleman (I have also downloaded the
popc.itp and lipid.itp).
When I do pdb2gmx -f popc128b.pdb -o popc128b.gro -p popc128b.top, I have the
error : POPC isn't in the database (ffG53a6.rtp).
I understand this error but I don't know what I must do. Indeed,  
pdb2gmx hasn't
commands for incorporate the popc.itp.
I read the manual and the gmx-users mailist and I don't find. So If  
you can help
me please.
Sorry for this very basic question.

King Regards.

Landry Charlier, PhD student
Lab. LCMBA, Dept of Chemistry
Team Chemometrics and Molecular Modeling
University of Nice, parc Valrose
06108 Nice Cedex2 France

----- End forwarded message -----

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