Your current alanine scanning MMPBSA.py input file is setup to perform
calculations on the complex, receptor, and ligand for only the mutant
(mutant_only=1). You should be able to use your previous results from your
wild-type calculations for comparison, but MMPBSA.py will not calculate
them again as long as you have mutant_only set to 1.
-Bill
On Sat, May 3, 2014 at 9:47 AM, Nitin Sharma <sharmanitin.nus.edu.sg> wrote:
> Dear amber users,
>
> I have already calculated binding free energy and energy decomposition by
> following protocol.
>
> &general
> startframe=1500, verbose=1,entropy=1,
> /
> &gb
> igb=2, qm_theory = 'PM3', saltcon=0.100
> /
> &decomp
> idecomp=2, dec_verbose= 2
> /
>
> Now I wish to do alanine scanning so I want to know do I have to calculate
> binding free energy again or I can use previous calculations to speed up
> the process by following process
>
> &general
> startframe=1500, verbose=1,entropy=1,
> /
> mutant_only =1,
> /
>
> Regards,
> Nitin Sharma
> Department of Pharmacy,Faculty of Science,National University of
> Singapore,block S7, Level 2, 18 science drive 4, Singapore 117543, Republic
> of Singapore: sharmanitin.nus.edu.sg<mailto:sharmanitin.nus.edu.sg> ;
> Phone +6582969643; http://www.linkedin.com/in/imsharmanitin
>
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>
--
Bill Miller III
Post-doc
University of Richmond
417-549-0952
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Received on Sat May 03 2014 - 12:30:02 PDT
