Re: [AMBER] Residue numbering

From: Sergio R Aragon <aragons.sfsu.edu>
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 [mailto:Daniel.Aiello.umassmed.edu]
Sent: Thursday, June 16, 2011 10:43 AM
To: amber.ambermd.org
Subject: [AMBER] Residue numbering

Hello,
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,
Dan

# 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.
#
DCTYPE 2
#
COMREC 35-41
COMLIG 175-180
COMPRI 35-41 175-180
RECRES 35-41
RECPRI 35-41
RECMAP 35-41
LIGRES 9-14
LIGPRI 9-14
LIGMAP 175-180

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber



_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 16 2011 - 12:30:05 PDT
Custom Search