On Mon, Mar 18, 2013 at 11:54 PM, Yew Mun Yip <yipy0005.gmail.com> wrote:
> Hi, I was conducting alanine scanning on a peptide with 26 residues with
> MMPBSA.py. The energy values obtained for the middle 24 residues were find,
> but when I mutated the terminal residues to alanine and conduct alanine
> scanning, the values were way too huge and the usual error message was
> observed:
>
> WARNING: INCONSISTENCIES EXIST WITHIN 1-4 NON-BONDED TERMS. CHECK YOUR
> INPUT FILES AND SYSTEM SETUP. THESE RESULTS MAY NOT BE RELIABLE (check
> differences)!
>
> Therefore, I wish to ask if there is a way to overcome this problem or
> terminal residues just can't be done with MMPBSA alanine scanning.
>
There must be some problem with it -- I don't think terminal mutations have
been attempted before, and I can't remember how that was handled by
MMPBSA.py.
What happens if you try to visualize the _MMPBSA_mutant_complex.mdcrd.0
file with your mutant topology file? Does it look reasonable?
> Thanks.
>
> --
> Regards
> Yip Yew Mun
> Graduate, Masters
> Chemistry and Biological Chemistry
> School of Physical and Mathematical Sciences
> Nanyang Technological University
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Mar 19 2013 - 08:00:03 PDT
