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
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> >
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--
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>
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Received on Sat Jan 14 2017 - 09:00:03 PST
