Hi Jason,
Something in the mutant ligand file was warped. I found out that it was
caused by a problem in the pdb file which then created an error in the
prmtop file for the ligand mutant. I corrected the mistake and everything
looks great now.
Thanks for the hint,
Jesper
-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
Sent: 28. april 2011 09:48
To: AMBER Mailing List
Subject: Re: [AMBER] MMPBSA.py error - VDW ****
Hi Jesper,
Can you visualize your trajectories? That is -- load the topology files and
intermediate trajectory files into VMD together to see if they're warped.
Specifically, try to visualize _MMPBSA_mutant_complex.mdcrd with your mutant
complex prmtop (and likewise for the receptor and ligand for both the mutant
and normal forms). Which structures look warped?
Thanks!
Jason
2011/4/28 Jesper Sørensen <lists.jsx.dk>
> Hi,
>
> I have performed a few ALA scanning calculations, and it works well
> for all but one mutation.
>
> When I look through the file "_MMPBSA_mutant_ligand_pb.mdout"
>
> I find lines with VDW values out of range spread out through the file:
>
> VDWAALS = ************* EEL = -45.9452 EPB =
> -939.3608
>
> It is a simple isoleucine to alanine mutation and this has worked for
> other residues that I have mutated.
>
> What can I do? Is there something that I am overlooking?
>
> I am using AMBER 11 and AMBERTOOLS 1.4
>
> Best,
> Jesper
>
>
>
>
>
> _______________________________________________
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> 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 Fri Apr 29 2011 - 02:00:03 PDT
