Re: [AMBER] trouble with

From: Chris Chris <>
Date: Fri, 18 Mar 2011 10:30:59 -0700 (PDT)


Would this be correct then? :

startframe=6000, endframe=8000, interval=1,
verbose=2, keep_files=0, receptor_mask=':1-28,:57-84',

From: Bill Miller III <>
To: AMBER Mailing List <>
Sent: Fri, March 18, 2011 12:50:17 PM
Subject: Re: [AMBER] trouble with

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
AMBER mailing list
Received on Fri Mar 18 2011 - 11:00:03 PDT
Custom Search