On Mon, Jul 23, 2012 at 9:41 PM, kamlesh sahu <kamleshsemail.gmail.com>wrote:
> Hello Jason,
>
> I used foloowing mmpbsa.in as input for binding energy calculation (one
> and
> two are residue names in the pdb file for C and D respectively) -
> Input file for running GB
> &general
> endframe=300, keep_files=2,
> receptor_mask= ":1-152", ligand_mask= ":153-304"
> strip_mask=":WAT:one:two:Cl-"
>
What are "one" and "two"? If these are not residue names, they will not
match anything in your trajectory. Furthermore, you should not have to
specify your receptor and ligand masks in this case. I would always
suggest *not* specifying a receptor/ligand mask and letting MMPBSA.py
figure it out on its own.
Only if your ligand residues are non-contiguous (e.g., if your ligand is
residues 1-2 and 5-8 in your complex topology file) or you have multiple,
identically-named ligands and don't want to automatically choose the *last*
one, should you revert to defining your own masks.
If MMPBSA.py fails to find a mask when you think it should, that indicates
that your topology files still have issues.
You can always use ante-MMPBSA.py to generate topology files for you, as
well.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Jul 23 2012 - 19:30:02 PDT
