I will give it a try. Thanks a bunch.
________________________________________
From: Jason Swails [jason.swails.gmail.com]
Sent: Thursday, June 16, 2011 3:15 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Residue numbering
Residues are numbered sequentially in the topology file. If you want to
number from a PDB file, use "ambpdb" to create a PDB file from your prmtop
and restart in order to compare.
HTH,
Jason
On Thu, Jun 16, 2011 at 11:42 AM, Daniel Aiello
<Daniel.Aiello.umassmed.edu>wrote:
> 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
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Jun 16 2011 - 13:00:03 PDT
