Thanks Jason for your reply.
one and two are the names of residues. Thank you for your suggestion. I
will figure out the location of ante-MMPBSA.py in my system and use it to
create topology files. I have read about this program in other emails of
amber mailing list but it looks like I dont have this program. I am using
amber10 and I got MMPBSA.py installed later on.
As suggested by you, I will create topology files using ante-MMPBSA.py and
then use these files without receptor and ligand masks to calculate binding
energies.
Thank you
Regards,
kamlesh
On Tue, Jul 24, 2012 at 11:27 AM, Jason Swails <jason.swails.gmail.com>wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Kamlesh Kumar Sahu (post doc researcher)
Riken, wako, Saitama, JAPAN
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Received on Mon Jul 23 2012 - 20:00:02 PDT
