Make sure you use ante-MMPBSA.py from AmberTools 12. The version from
AmberTools 1.5 is unreliable.
All the best,
Jason
On Mon, Jul 23, 2012 at 10:42 PM, kamlesh sahu <kamleshsemail.gmail.com>wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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 - 21:00:02 PDT
