[gmx-users] Problem with restraint in lipid membrane

[David]

On Sun, 2003-01-19 at 15:59, Francesco Tordini wrote:
> Hi gmx users,
> i'm tryng to do some energy minimization with position restrain on all
> heavy atoms in every dppc and dppe residue in my membrane system (an
> edited version of dppc64.pdb with mixed dppc/dppe residues).
> When i launch grompp, i get the following error: 
> 
> Fatal error: [ file "posre.itp", line 54 ]:
>              Atom index (51) in position_restraints out of bounds (1-50)
> 
> I've searched the Mailing list, and also read the WARNING (genpr only
> works for the first molecule... ") in genpr's man pages, but, despite 
> my many attempts, i'm not still able to resolve the problem.
> In fact, i don't understand how to manage the file (or many files?) 
> posre.itp in a system like this.
You should make separate posre files for DPPE and DPPC, since they have
a different number of atoms. Did you modify your topology to get the
correct order for your lipids? Names in the coordinate file are *not*
used for identification, the topology is authorative.

> 
> Cheers
> 
> Franz
> 
> 
> =======================================
> 
> Francesco Tordini
> Laboratorio di Modellistica Molecolare
> Università degli studi di Milano Bicocca
> 20126 Milano - Italy
> 
>  <tordini at tiscalinet.it>
> 
> =======================================
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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