AMBER Archive (2009)

Subject: [AMBER] periodic boundary condition for implicit solvent simulation and SHORT command

From: Workalemahu Berhanu (
Date: Thu Sep 10 2009 - 17:37:32 CDT

Dear amber users

I have a protein ligand complex pdb file and I would like to do the implicit
solvent simulation with periodic boundary condition to keep the lignad close
to the protein and observe the interaction between the peptide and the
ligand. Is it possible to do periodic boundary condition using implicit
solvent simulation with amber? I also would like to learn how to do
restrain on some inter atomic distance say the central atom of the ligand
and the reside of the peptide which is close to the ligand. In the amber
manual I read about the command SHORT. Could you please explain to me about
this command and could you please give me your advice and some example on
how to use it for restraining the peptide and the ligand using specific
atoms and residues and keeping the distance between the ligand and the
protein with certain range say 4 to 12 angstrom?

Thank you

With best regards

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