[gmx-users] ligand isomerisation
feenstra at chem.vu.nl
Wed May 14 09:56:01 CEST 2003
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.
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
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