Hi Robert:
Sorry, I made some mistake. The patch fixed some other bug in
per-pair decomposition, not for your problem. The explanation you
found is the right.
Denis
2012/8/28 Deák Robert <kokumetto.gmail.com>:
> 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
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
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Received on Mon Aug 27 2012 - 18:00:03 PDT
