MMPBSA.py has a built-in guesser that should be able to determine the
residues that apply to the ligand and receptor, as long as there is only one
part to the ligand and the topology files are correctly provided on the
command line. If, for some reason the guesser does not work, then you can
specify the residues explicitly in the &general namelist using the
receptor_mask and ligand_mask variables, using standard AMBER procedures to
define the masks. See the manual for more details.
-Bill
On Wed, Jul 14, 2010 at 1:48 AM, Amor San Juan <amorsanjuan.yahoo.com>wrote:
> Hi all,
>
> Has anyone did try running mmpbsa.py with input file of two different parts
> of receptor (numbering not consecutive) and also one ligand part ? In
> previous use of mmpbsa.pl the treatment of numbering is by specifying two
> parts of RSTOP, RSTART. Like this way:
>
> LSTART
> LSTOP
> RSTART
> RSTOP
> RSTART
> RSTOP
>
> Could anyone help on this with mmpbsa.py?
>
> Amor
>
>
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>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Wed Jul 14 2010 - 03:30:05 PDT
