Dear Jason Swails,
Thank you for your reply.
Initially I was doing the calculation with the mm_pbsa.pl version.
I don't know, how it worked with the tutorial and not for my case of
protein-ligand.
Now, according to your suggestion, I am trying for the Python version.
But as I can see, this is the MPI version need to be installed.
However, I am doing my calculation in my single processor PC, with the
Amber10 installed in.
So, can you please let me know how to install the Python version and what
will be the steps to be followed for the installation of mpi4py and the
usage of MM-PBSA.MPI.py.
Thanks in advance for your suggestions.
Siddharth
On Wed, Sep 8, 2010 at 11:11 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Hello,
>
> Have you considered trying the Python version? The source code and
> instructions for installation/use are included on the same tutorial you're
> using now (http://ambermd.org/tutorials/advanced/tutorial3/py_script). If
> you choose to use that version, please remember to apply the patches also
> located on that site.
>
> Good luck!
> Jason
>
> On Wed, Sep 8, 2010 at 8:49 PM, Siddharth Rastogi <
> siddharthrastogi08.gmail.com> wrote:
>
> > Hello Bill Ross,
> >
> > Thank you for your response and the suggestions.
> >
> > However, if I am going to the AMBER tutorial-3 regarding the MM-PBSA
> > calculation, I can see the use of gas phase topology (prmtop) files in
> the
> > extracts_coords.mmpbsa and binding_energy.mmpbsa files with the use of
> > "ras-raf_solvated.prmtop"
> > to generate the trajectory files.
> >
> > Also, I wonder how these works in the tutorial. I am a bit confused with
> > this. If I am wrong, rectify me.
> >
> > Does your trajectory files (prod_1.mdcrd, prod_2.mdcrd...) contain water
> > molecules ?
> >
> > I just wanted to calculate the binding free energy between the
> > protein-ligand complex of a solvated system. Please do suggest me the
> right
> > path.
> >
> > Thanks
> > Siddharth
> >
> >
> > On Fri, Sep 3, 2010 at 8:14 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> >
> > > > FATAL: NATOM mismatch in coord and topology files.
> > >
> > > The prmtop for a solvated system cannot be used with crds for the
> vacuum
> > > version and vice-versa.
> > >
> > > Bill
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Siddharth Rastogi
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Siddharth Rastogi
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Received on Tue Sep 14 2010 - 10:00:03 PDT
