[gmx-users] distance constraints

Michal Kolinski mkolin at iimcb.gov.pl
Mon Feb 20 18:39:37 CET 2006

thank you for help :)

There is no Gromacs tool to do this (yet), but there are some scripts 
around to merge .top or .itp files.
I'll attach one I have written a long time ago, so don't laugh about the
style. It still works fine for me. You also need to merge the coordinate
files (.pdb or .gro or whatever). I also have a script for this somewhere.
Let me know if you need it.


Michal Kolinski wrote:

> Thank you for advice.  In my case I have receptor protein with a 
> ligand inside the active site of the receptor.  
> I need to constrain distance between one of the receptors atom and one 
> of the ligands atom to
> force a proper orientation of the ligand during the simulation.  As I 
> understand  I have to
> combine both topologies (for receptor and ligand) and then put it in a 
> single *.tip file. 
>  Is there a simple way to  rewrite/renumber all the atoms of the ligand?
> Michal
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