Thanks bill
-----Original Message-----
From: Bill Miller III [mailto:brmilleriii.gmail.com]
Sent: Sunday, May 04, 2014 3:04 AM
To: AMBER Mailing List
Subject: Re: [AMBER] alanine scanning
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 Sun May 04 2014 - 09:00:03 PDT
