Re: [AMBER] Ala double mutation scans

From: Jesper Sørensen <>
Date: Fri, 8 Jul 2011 09:24:42 +0200

Thanks Dwight I will give it a go.

Essentially, if I just made all the input files (mdcrd etc.) myself
"manually" in ptraj and leap, and feed these into, there shouldn't
be a problem, right?


-----Original Message-----
From: Dwight McGee []
Sent: 6. juli 2011 17:01
To: AMBER Mailing List
Subject: Re: [AMBER] Ala double mutation scans


If you wanted to make multiple mutations, the *perl version* of MMPBSA does
allow for this. If you instead wanted to use the *python version* of MMPBSA
and run a double alanine scanning calculation it would in essence take two
steps. Step 1 would be mutating one residue to Ala and allowing to
make the mutant mdcrd. Step 2 would be taking the new mutant mdcrd created
in the previous step and reading it into using the (-y) flag ( be
sure to use the correct topology files matching the mutant mdcrd) so
therefore it will make the second mutant mdcrd, which will in essence have
the double mutation you want. The tricky part is that you will have to
create two new topology files, one containing the single mutation and the
other one that has the double mutation. Hopefully this should work.

2011/7/6 Jesper Sørensen <>

> Hey all,
> I know that isn’t set up for double ala-scanning
> calculation, but wouldn’t I be able to make the required files
> manually and then just feed these into using the right keywords
in the input file?
> I know that double mutations are probably stretching the methods
> accuracy quite a bit as two mutations close together will probably
> alter the dynamics, but I’d like to give it a go anyways.
> Are there alternative ways to do it? Like running one ala scan
> calculation and then running a second one on the “new” trajectories
> formed by
> And then just adding up the results?
> Best regards,
> Jesper
> _______________________________________________
> AMBER mailing list

T. Dwight McGee Jr.
Quantum Theory Project
University of Florida
Graduate Student
"Problems cannot be solved at the same level of awareness that created
                Albert Einstein
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Received on Fri Jul 08 2011 - 00:30:04 PDT
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