It seems reasonable to script it (using python or perl or maybe even bash
with sed/awk). I don't know of any programs off-hand that can do bulk jobs
like this (which lends this to scripting).
Energy decomposition typically gives very similar results from what I've
heard, so it may be worth trying that out (though for MMPBSA.py, amber11 is
needed since decomp does not work correctly with imin=5 in sander10 or
earlier).
Good luck!
Jason
On Mon, May 31, 2010 at 8:11 PM, Rilei Yu <yulaomao1983.yahoo.com.cn> wrote:
> Dear amber users,
>
> I used manually edit the native pdb file to obtain the prmtop files of the
> mutants. For example, I usually deleted the side chain of the native
> residues. That is a bit of time consuming, especially, when you try to do
> ala scanning on big system. Can anyone here give me more convenient way to
> do this job? Or the program can do it automatically?
>
> Very thanks!
>
> Rilei Yu
>
>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon May 31 2010 - 18:00:04 PDT
