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
>>>
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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 - 09:00:04 PST
