Dear Denis,
The second question still remaines. How can run energy decomposition in
amber12?
What are the changes relative to amber11?
Robert
2012/8/28 Liu Denis <cndenis.gmail.com>
> 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
> >>
> >>
> >>
> >> --
> >> ----GnuPG Public Key----
> >> Key ID: 0x488C9571
> >> Fingerprint: C292 D888 D713 4D13 57F0 C07D 16F3 10C9 488C 9571
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> ----GnuPG Public Key----
> Key ID: 0x488C9571
> Fingerprint: C292 D888 D713 4D13 57F0 C07D 16F3 10C9 488C 9571
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Aug 28 2012 - 03:30:06 PDT
