[gmx-users] Problem with restraint in lipid membrane

[K.A. Feenstra]

David wrote:
> 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.

Additionally, the atom numbers of the position restraints refer to
the numbers in the *atom* *type* definition, which explains why
you should only go up to 50 atoms; consequently, the definition will
always be used for *all* the molecules of the same type, i.e. for
all DPPE, or all DPPC molecules (or, e.g. all SPC waters).


-- 
Groetjes,

Anton
  ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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