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

From: Liu Denis <>
Date: Tue, 28 Aug 2012 00:47:12 +0800

Hi Robert,

We just talked about the your first question in

In your second question, could you find error message in mdout file?


2012/8/27 Deák Robert <>:
> 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
> error.
> "
> 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?
> Thanks,
> Robert Deak
> _______________________________________________
> AMBER mailing list

----GnuPG Public Key----
Key ID: 0x488C9571
Fingerprint: C292 D888 D713 4D13 57F0  C07D 16F3 10C9 488C 9571
AMBER mailing list
Received on Mon Aug 27 2012 - 10:00:02 PDT
Custom Search