Re: [AMBER] Residue numbering

From: Sergio R Aragon <>
Date: Thu, 16 Jun 2011 19:01:29 +0000

Hello Dan,

Tleap does not renumber residues when you first load a pdb file into it, but it does renumber residues when you save a pdb file from within it. This is easy to try out for yourself with
Any pdb file.

Cheers, Sergio

-----Original Message-----
From: Daniel Aiello []
Sent: Thursday, June 16, 2011 10:43 AM
Subject: [AMBER] Residue numbering

My ultimate goal is to compute binding energies for protein receptor-ligand complexes on a per residue basis. A lot of times the residue number for the first residue in my pdb file is not one. In addition, I have pdb files that have been modified such that the residue numbering is not sequential. How does tleap handle this? Does tleap re-assign sequential numbers to residues starting from one? This will impact how I set up my parameter file for mm_pbsa. Should I use the original pdb numbering or should I assume that tleap re-numbers the residue numbers? Thanks for your help,

# COMREC - Residues belonging to the receptor molecule IN THE COMPLEX.
# COMLIG - Residues belonging to the ligand molecule IN THE COMPLEX.
# RECRES - Residues in the receptor molecule.
# LIGRES - Residues in the ligand molecule.
# {COM,REC,LIG}PRI - Residues considered for output.
# {REC,LIG}MAP - Residues in the complex which are equivalent to the residues
# in the receptor molecule or the ligand molecule.
COMREC 35-41
COMLIG 175-180
COMPRI 35-41 175-180
RECRES 35-41
RECPRI 35-41
RECMAP 35-41
LIGMAP 175-180

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Received on Thu Jun 16 2011 - 12:30:05 PDT
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