[gmx-users] ligand isomerisation

[Anton Feenstra]

Chris Shaw wrote:
> Hi all, 
> I have a ligand (retinal) which can exist in two conformational isomers. 
> I know the parameters (ie angles, dihedrals etc) of both conformations,
> but how can I get gromacs to change the conformation of retinal from one
> form to another. I have tried
> grompp -r option with ie -c conformer1 ret -r conformer2 ret
> ,but nothing happened the retinal just stayed in the conformer1 form.
> Am i missing something obvious?? 

Yes: grompp -r does not switch on position restraints. You have to do that
in your topology by adding a [ position_restraints ] section, or include
the posre.itp file that you might already have.


-- 
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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