[AMBER] Decomposing the free energy contributions to the binding free energy

From: Deák Robert <kokumetto.gmail.com>
Date: Mon, 27 Aug 2012 09:55:17 +0200

Dear AMBER users,

I have some questions about AMBER tutorial A3, mainly about decomposition
of free energy.

1.) I did exactly the same decomposition of binding energy of RAS-RAF, as
described on section 3.6 for Per-residue decomposition, but taking into
account all residues of the receptor and the ligand too. I expected, that
the sum of TOTAL energies for residues (from FINAL_DECOMP_MMPBSA.dat) will
got the binding free energy (from FINAL_RESULTS_MMPBSA.dat). This is true
for GB, but not for PB method.

Could somebody explain me why?

2.) I tried to do the same work with AMBER12, but every time I've got an
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
sander found! Using /usr/local/amber11/bin/sander
mmpbsa_py_energy found! Using /usr/local/amber11/bin/mmpbsa_py_energy
cpptraj found! Using /usr/local/amber11/bin/cpptraj
Preparing trajectories for simulation...
50 frames were processed by cpptraj for use in calculation.

Beginning GB calculations with /usr/local/amber11/bin/sander
  calculating complex contribution...
CalcError: /usr/local/amber11/bin/sander failed with prmtop ras-raf.prmtop!
Exiting. All files have been retained.

AMBER11 did the work with exactly the same ras-raf.prmtop.

Could somebody tell me what to do?

Robert Deak
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Received on Mon Aug 27 2012 - 01:00:03 PDT
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