Re: [AMBER] Single-Point MM-PBSA/GBSA Energy Calculations

From: Hai Nguyen <>
Date: Sat, 14 Jan 2017 11:31:01 -0500


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 -i ../ -cp ../../{pdb_folder}/prmtop -y ../../

Otherwise, you can look at pytraj (AmberTools16) tutorial to get energy (by
calling pysander)

hope this help

On Sat, Jan 14, 2017 at 11:20 AM, Naiem Issa <> wrote:

> Hello,
> I wanted to see if it is possible to perform single-point energy
> calculations for MM-PBSA/GBSA using 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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Received on Sat Jan 14 2017 - 09:00:02 PST
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