There is a tutorial :
http://ambermd.org/tutorials/advanced/tutorial3/
Jing
On Sat, Jan 14, 2017 at 6:55 PM, Nhai <nhai.qn.gmail.com> wrote:
> I suggest to read manual carefully.
>
> We have similar project here
> https://github.com/kmb413/CADRES/blob/master/BlindDataset_DDG/methods/10.
> run_mmgbsa.py
>
> Hai Nguyen
>
> > On Jan 14, 2017, at 11:38 AM, Naiem Issa <naiem.issa.gmail.com> wrote:
> > Hello Hai,
> >
> > Thanks. Just wanted to calculate free energies of binding. I am familiar
> > with prmtop for topologies but didn't realize had to do rst7. Would you
> > have to supply receptor and ligand inidividually in addition to the
> complex
> > for these calculations? Could you give a very basic example of what would
> > be in our mmpbsa.in?
> >
> > Very helpful.
> >
> > -N
> >
> >> On Sat, Jan 14, 2017 at 11:31 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> >>
> >> hi,
> >>
> >> what type of "single-point energy calculations" do you need?
> >>
> >> Normally you need to convert pdb files to prmtop and rst7 format then
> pass
> >> them to MMPBSA program.
> >> It can access a list of rst7 files
> >>
> >> e.g from what I did
> >> MMPBSA.py -i ../mmgbsa.in -cp ../../{pdb_folder}/prmtop -y ../../
> >> {pdb_folder}/no_restraint_new_protocol/min_NoH_*rst7
> >>
> >> Otherwise, you can look at pytraj (AmberTools16) tutorial to get energy
> (by
> >> calling pysander)
> >> http://amber-md.github.io/pytraj/latest/tutorials/
> >> energy_decomposition.html
> >>
> >> hope this help
> >> Hai
> >>
> >>> On Sat, Jan 14, 2017 at 11:20 AM, Naiem Issa <naiem.issa.gmail.com>
> wrote:
> >>>
> >>> Hello,
> >>>
> >>> I wanted to see if it is possible to perform single-point energy
> >>> calculations for MM-PBSA/GBSA using MMPBSA.py in Amber. I have
> thousands
> >> of
> >>> protein-ligand complexes that were obtained via docking and would now
> >> like
> >>> to perform single-point energy calculations on the final docked
> >> complexes.
> >>> Is there a way to do this directly on the complexes without having to
> do
> >> MD
> >>> simulations and obtaining trajectories? Apologies for the very basic
> >>> question as I am new to this.
> >>>
> >>> Thanks,
> >>> Naiem
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Naiem T. Issa
> > M.D./Ph.D Candidate, Tumor Biology
> > Georgetown University School of Medicine
> > Howard Hughes Biomedical Research Scholar
> > Tel: 703.587.1315 E-mail: nti.georgetown.edu <nti.georgetown.edu>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
----------------------
Dr. Jing Huang
*Institute of Chemistry and the Lise Meitner-Minerva Center for
Computational Quantum*
*Chemistry, Hebrew University of Jerusalem, Givat Ram Campus, Jerusalem
91904, Israel*
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jan 14 2017 - 09:00:05 PST
