Jason
Thanks for that, I've already checked for ions and the strip mask is removing exactly what I expect it to and nothing more.
Thanks anyway
Nick
Nicholas Rakowski
Email: nickkowski.yahoo.co.uk
________________________________
From: Jason Swails <jason.swails.gmail.com>
To: Nick Rakowski <nickkowski.yahoo.co.uk>; AMBER Mailing List <amber.ambermd.org>
Sent: Tuesday, 21 February 2012, 22:41
Subject: Re: [AMBER] Issue with mmpbsa
Do you have any ions or waters that you're trying to keep? I've never seen
this issue before unless there's _something_ happening in which atoms are
either kept or not kept which the user didn't expect. Look at the default
value for strip_mask for MMPBSA.py and compare that to the atoms you expect
to delete or keep in your topology files.
I don't realy think I have enough information to make too many guesses...
HTH,
Jason
On Tue, Feb 21, 2012 at 8:58 AM, Nick Rakowski <nickkowski.yahoo.co.uk>wrote:
> Amber Users
>
> I'm attempting to run a mmpbsa/gbsa calculation on a ligand, receptor
> system. I have all the required parmtops - solvated complex, complex,
> receptor and ligand and a 10 nsec MD run. Before running the scripts my
> system is intact and visualization shows no issues. Once the co-ordinates
> are extracted, the receptor is fine, and the ligand is mostly intact.
> However, a sugar ring in the ligand is completely mangled. This occurs with
> both Python and Perl scripts. I am using Amber 10.0 - does anyone have any
> suggestions?
>
> I have already checked the naming conventions, and tried reproducing the
> parmtop files. Why does it only affect 1 sugar ring, when the rest of the
> ligand is ok?
>
> Thanks in advance
>
> Nicholas Rakowski
> Email: nickkowski.yahoo.co.uk
> _______________________________________________
> 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 Wed Feb 22 2012 - 00:00:02 PST
