[AMBER] GBSA calculations using mm_pbsa.pl

From: manikanthan bhavaraju <manikanthanbhavaraju.gmail.com>
Date: Sat, 26 Mar 2011 19:59:38 -0500

I am trying to calculate binding energy of the protein+ligand with GBSA
using Amber11. The snapshots were successfully extracted for the last 5ns.
Previously the complex system was minimized and equilibrated under explicit
slovent method using Amebr8 and ff99 forcefield. The binding energy(MMPBSA
and GBSA) and decomposition calculations were successfully calculated using
Amber8. Now I want to compare the results of Amber8 with Amber11.

I am running GBSA calculation using Amber11 in parallel on 4 processors.
The mm_pbsa.pl has analyzed only complex snapshots and generated
binding_energy.mmgbsa.log, snapshot_rec.in, snapshot_com.in snapshot_lig.in,
and snapshot_com.all.out. The job is still running but nothing else is
written to the .log file and receptor, ligand snapshots were not analyzed
for the GBSA calculations.

Any help is really apperciated.


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Received on Sat Mar 26 2011 - 18:30:02 PDT
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