[gmx-users] How to apply distance restraints.

Kirti Patel kirti at chem.iitb.ac.in
Fri May 13 11:37:35 CEST 2005

Hi everybody,

I am working on a peptide which mainly contains hydrophobic amino acids and histidines. I want the
four histidines present in my peptide to be restrained in a tetrahedral geometry. For these I
applied distance restraints which I included in topology file and also in vac.mdp, heat.mdp and
cool.mdp (as I intend to do simulated annealing). But still the restraints are not applied in the
peptide and histidines remain on the periphery of the peptide after folding.

Any suggestions are most welcome.



Kirti Patel
"Research Scholar"
Bio-organic Lab,                     Room No. c307
Department of Chemistry,             Hostel 12
                   Indian Inst. of Technology
Ph. No.-022-25764780(Lab),
Fax No:-022-25767152

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