Re: [AMBER] MMPBSA-binding energy calculation

From: Hirdesh Kumar <>
Date: Tue, 21 Jun 2011 21:39:46 +0530

You need to provide the protein structure without bound ligand for mmpbsa
analysis. You can do so either using ptraj or simply by tleap using the
same files which you have used previously for system preparation but
excluding ligand information from complex this time to generate parameter
and coordinate file for protein atoms only.


On Tue, Jun 21, 2011 at 7:55 PM, baljinder <> wrote:

> Dear all,
> We are calculating the binding free energy using two steps viz. extraction
> of coordinates and binding free energy calculation.
> While doing the second step the error message i am getting is "
> odd number of probe positions on torus!
> /root/amber/amber10/exe/sander -O -i -o
> sander_rec.1.out -c ./snapshot_rec.crd.1 -p ./receptor-vac.prmtop not
> successful
> "
> We tried to increase the PRBRAD from 1.4 to 1.6, but the same error
> message.
> While trying to make pdb from extracted coordinate we are not able to make
> PDB from extracted cordinated of receptor, while for complex and ligand
> there is no such problem. The mistake from my side is initially i dint
> saved
> the receptor (protein only without ligand)prmtop along with ligand and
> complex, saved it separetly .
> Kindly suggest the solution if possible.
> Thanks in advance
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Received on Tue Jun 21 2011 - 09:30:04 PDT
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