Re: [AMBER] trouble with

From: Bill Miller III <>
Date: Fri, 18 Mar 2011 12:50:17 -0400

Since the ligand residues are not sequential, will not be able to
guess the proper residue numbers, so you will need to specify these by hand
using the receptor_mask and ligand_mask variables in the input


On Fri, Mar 18, 2011 at 12:44 PM, Chris Chris <> wrote:

> I am trying to perform mmpbsa analysis using the python version of the
> program
> on the complex in the attachment but have been unable to do so.
> As can be seen in the complex scematic, the ligand and receptor are not
> sequentially numbered. I thought this might be a problem so when I made the
> topology files, I kept the numbering as it was in the original pdb which
> was
> used to make the topology files in xleap.
> This was to no avail. Can anyone tell me what is going on here? Do I have
> to
> specify the residues in my .in file (see attached)?
> Thanks for any advice, I have also attached the .err and .out files as well
> _______________________________________________
> AMBER mailing list

Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Fri Mar 18 2011 - 10:00:05 PDT
Custom Search