> On Dec 23, 2013, at 5:39 AM, suma jayakrishnan <sumajayakrishnan.jk.gmail.com> wrote:
>
> Dear AMBER users,
>
> Is it possible to do computational alanine scanning of
> phosphorylated residues using alanine scanning code in amber11? I
> tried the alanine scanning methods for calculating the binding free
> energy when phosphorylated serine mutated to alanine, but it gives
> error. How can I over come this problem? Is there any other method for
> doing this?
The current code does not support this. If you can understand what is being done inside alamdcrd.py then you can add code to handle phosphorylated residues.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Dec 23 2013 - 06:00:03 PST
