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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Received on Wed Sep 08 2010 - 20:30:05 PDT
