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

From: Deák Robert <kokumetto.gmail.com>
Date: Mon, 27 Aug 2012 21:52:12 +0200

Dear Denis,

Thank you the answer.

Regarding to the first problem: How could I use this patch? Is it for
AMBER12?
In the meantime I got an explanation to my problem in the tutorial (for
AMBER11), namely:
"PB non-polar solvation energies are currently not decomposable"
http://ambermd.org/tutorials/**advanced/tutorial3/py_script/**section6.htm<http://ambermd.org/tutorials/advanced/tutorial3/py_script/section6.htm>
I dont fully understand the patch, but this can fix this problem?

For the second problem, the only mdout file I have is attached with the
progress.log too. I have made it with amber12 (and just amber12 is
installed on that machine) but the mdout starts with reference to amber11
...
The only difference I have made to the tutorial mentioned above is
dec_verbose=3. (With AMBER11 it worked on another machine.)

Robert

2012/8/27 Liu Denis <cndenis.gmail.com>

> Hi Robert,
>
> We just talked about the your first question in
> http://archive.ambermd.org/201208/0315.html
>
> In your second question, could you find error message in mdout file?
>
> Denis
>
> 2012/8/27 Deák Robert <kokumetto.gmail.com>:
> > 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
> > _______________________________________________
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>
>
>
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Received on Mon Aug 27 2012 - 13:00:03 PDT
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