On Wed, Sep 19, 2012 at 8:27 AM, Dilraj LAMA <dilrajl.bii.a-star.edu.sg>wrote:
> Dear Amber users,
> I am currently familiarizing myself with the
> MMPBSA.py script using Amber12. I have couple of queries in this regard.
>
> FIRST:
>
> There is an issue with the decomposition calculation.
>
> My input script for the calculation is:
>
> ------------------------------------------------------------------
> &general
> startframe=1, endframe=10, interval=5,
> verbose=2, keep_files=2,
> /
> &gb
> igb=5, saltcon=0.150,
> /
> &decomp
> idecomp=2, dec_verbose=0,
> print_res="191-204"
>
If you use "csv_format=0" in the &decomp section, you get the ASCII output
file format that is the same as AmberTools 1.5.
> /
> ---------------------------------------------------------------------
>
> In this case, The GB calculation went of fine, but There was nothing
> written on the decomp.out file and there is no specific error message.
>
Can you send me 2 frames of your trajectory and the input files so I can
try to reproduce this? print_res should behave the same in Amber12 and
Amber11 (and to my knowledge, it did).
> SECOND:
>
> I am also trying to do the alanine scanning. I could run a test
> successfully with a single Alanine mutant. I was wandering if it is
> possible to run a double alanine mutant? I read in the mailing list
> that this is possible with MMPBSA.pl but not currently with MMPBSA.py.
> Is this is the case? Is there a way around doing this?
>
As Bill said, we only support single alanine mutants. But you can take the
_MMPBSA_mutant_complex.mdcrd file that's printed during the first mutation
and mutate it again :).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Sep 19 2012 - 07:00:03 PDT
