Can you send the necessary prmtop files, along with your MMPBSA.py input
file and a small trajectory file that results in the mangled coordinates
you are describing? Let's see if we can reproduce your errors.
-Bill
On Wed, Feb 22, 2012 at 2:43 AM, Nick Rakowski <nickkowski.yahoo.co.uk>wrote:
> 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
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Fri Feb 24 2012 - 13:00:03 PST
