[AMBER] MMPBSA-binding energy calculation

From: baljinder <baljinder7.gmail.com>
Date: Tue, 21 Jun 2011 19:55:51 +0530

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 sander_rec.in -o
sander_rec.1.out -c ./snapshot_rec.crd.1 -p ./receptor-vac.prmtop not

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 - 07:30:05 PDT
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