[gmx-users] Position restraints for two groups

[Anton Feenstra]

Sergio Manzetti wrote:
> I'd like to add posres on two groups defined in the index file. The 
> index file was made with the gro file from the pdb2gmx. I use genpr with 
> the input  *gro  file for EM  and the ndx file to generate position 
> restraint for one group first and the second in a new genpr session. 
> Then I merge the two *itp to one file. However, I get:
> 
> Cleaning up temporary file gromppa20162
> Fatal error: Invalid order for directive position_restraints, file 
> ""drg.itp"", line 3

Position restraints are a molecule property in Gromacs. Therefore, the
[ posres ] section *must* appear inside the appropriate [ moleculetype ]
section. You should also be aware, that this means you must use molecule
internal atom numberings (i.e. 1, 2 and 3 for e.g. water), and that *all*
molecules of that type will be restrained. This also means that the numbers
genpr generates from your .gro file will only be correct for the first
molecule in your .gro file, which usually is the protein.

So, it appears you want to posre your ligand molecule. You should do that
as follows:
1) make a sepate .gro (or .pdb) file of only your ligand
2) use that file and genpr to create the posre.itp file for the ligand
3) in your .top file, first include the ligand topology (e.g. drg.itp),
    and immediately after that include the posre.itp for the drug, like:
#include "drg.itp"
#ifdef POSRE_DRG
#include "posre_drg.itp"
#endif

(Alternatively, you could put the ifdef/include posre inside the drg.itp file.)


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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