AMBER Archive (2003)

Subject: anal, amber7 and resnum 0

From: Sanjeev B.S. (sanjeev_at_mbu.iisc.ernet.in)
Date: Fri May 16 2003 - 17:15:19 CDT

Hello,
        I am using anal from amber7 to calculate interaction energy
between a subtrate and its ligand. The starting crystal structure began
with residue number zero and there were totally 135 residues. Two residues
thereafter are ligand's. When I define groups as 'RES 1 135' and
'RES 136 137', I get into problem. I actually find the number of atoms
being tallied correctly with 'RES 135 136'! If I give 'RES 0 134' it
doesnot define a group! If I give 'RES 1 1' it shows 24 atoms, and that is
neither the number of 0'th residue or 1st residue from generated PDBs!

        I would be grateful if anyone suggests me a work around for this
problem. With other set of ligand-substrate docking I had no problems, but
only with ligands with this substrate.

Thanks in advance,
-Sanjeev