Re: [AMBER] Alanine scanning with CYS

From: Guenegou, Guillaume [ORDFR] <>
Date: Wed, 1 Jun 2011 13:42:05 +0200

Sorry, I did not precise I use with amber11.
So I have to write atom numbers in the input file.
The question could be: the MUTANT_ATOM1 has to be SG for CYS (as OG for

-----Original Message-----
From: Bill Miller III []
Sent: mercredi 1 juin 2011 12:48
To: AMBER Mailing List
Subject: Re: [AMBER] Alanine scanning with CYS

I believe it should work with both and, but I know
it will work with And with, you do not need to
any pointer atoms in the input file. will determine which
you want mutated based on the provided prmtop files, so there is really
atom information you need to provide about the mutated residue.

I hope that helps.


On Wed, Jun 1, 2011 at 4:53 AM, Guenegou, Guillaume [ORDFR] <> wrote:

> Dear all,
> I would like to run trials with alanine scanning. I understand why
> are special cases. But I do not understand why there is no precision
> about CYS in documentation whereas SER (similar to CYS) is treated.
> Do I have to make an extrapolation for CYS? Or its case is not
> Thanks for any answers,
> _______________________________________________
> AMBER mailing list

Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
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Received on Wed Jun 01 2011 - 05:00:02 PDT
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