[gmx-users] Help

Justin A. Lemkul jalemkul at vt.edu
Sun Jul 6 15:42:48 CEST 2008

Maryam Nikoosaleh wrote:
> Dear all,
> I have a question about restraint. How can I restrain the ligand of 
> one protein? I know how to restrain  atoms of one protein.But when 
> protein has several ligands, gmx  genaretes  different *.itp files  
> for  their topologies and when I enter restraints in topology file , 
> gmx gives me this error :
> "Atom index (821) in constraints out of bounds (1-1).
> This probably means that you have inserted topology section "constraints"
> in a part belonging to a different molecule than you intended to.
> In that case move the "constraints" section to the right molecule."

First, constraints are different from restraints in Gromacs.  If you 
want to *restrain* the position of your ligand, use position 
restraints.  You can create a posre.itp for your ligand using genpr 
(making individual ligand .itp files if you have multiple), then include 
it in your system topology, i.e.:

#include "ligand_posre.itp"

Also, as a general note, search the list archive before posting, as I 
know I have seen this error before.  Choose an informative subject line 
for your messages to attract the attention of someone who might know how 
to help.  Many emails with "help" as the subject line get ignored, 
because it is often assumed that the answer can be found in the manual, 
list archive, or wiki.


> I don't want to freez this part of protein,b/c I  want to optimize 
> this part of protein.
> please answer me.
> Thnaks , Maryam 
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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