AMBER Archive (2003)

Subject: Re: anal, amber7 and resnum 0

From: David A. Case (case_at_scripps.edu)
Date: Fri May 16 2003 - 16:57:33 CDT

On Sat, May 17, 2003, Sanjeev B.S. wrote:

> 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!

Anal uses the residue numbering in Amber, which always starts at 1. This
numbering may not match what was in the original pdb file. You can look at
the prmtop file you are using to see both the the residue order and numbers,
and the number of atoms per residue. Alternatively, use ambpdb to generate a
pdb file, and look at that.

..good luck...dac 

-- 

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