On Mon, Feb 11, 2013 at 12:04 AM, WenJuan Huang <hwjamber.gmail.com> wrote:
> Hello Mani,
>
> Are you using amber12?
>
> This error is not any happened to systems with metal ions, it also happend
> to my calculations when I using amber12.
>
> MM-GBSA works fine with MMPBSA.py script. However, MM-PBSA keep giving me
> the same error as yours. Here is a sample out put file of my calculation:
>
> Reading command-line arguments and input files...
> Loading and checking parameter files for compatibility...
> mmpbsa_py_energy found! Using
> /global/software/amber-12/bin/mmpbsa_py_energy
> cpptraj found! Using /global/software/amber-12/bin/cpptraj
> Preparing trajectories for simulation...
> 10 frames were processed by cpptraj for use in calculation.
>
> Beginning GB calculations with
> /global/software/amber-12/bin/mmpbsa_py_energy
> calculating complex contribution...
> calculating receptor contribution...
> calculating ligand contribution...
>
> Beginning PB calculations with
> /global/software/amber-12/bin/mmpbsa_py_energy
> calculating complex contribution...
> CalcError: /global/software/amber-12/bin/mmpbsa_py_energy failed with
> prmtop 3MBP-c.top!
> Exiting. All files have been retained.
>
> There are other people posted similar situations in last year and people
> replys that the MMPBSA.py code in amber12 had major modifications that they
> wasn't sure what is going on. Therefore, I do think it is a problem in the
> script not due to a specific system.
>
The changes to the code have been reorganization, not functional changes.
MMPBSA.py (as well as any MM/PBSA script) still writes input files for
external programs and runs those programs. The bulk of the 'problems' have
been poor error reporting (which have been systematically improved as
people reported problems that were not clearly explained in the error
message).
If you build AmberTools 12 with all of the available bug fixes, you should
get an error message about why the MM/PBSA simulations are not working.
Most of the cases of the PB part failing is due to changes in the PBSA
defaults from version 11 to version 12. In particular, the non-polar
solvation free energy method (inp) had its default changed from 1 (where
radii are used from the topology file; radiopt=0) to 2 (where radii are
determined inside the PBSA source code; radiopt=1). The principle problem
that people have here is that the radii for one or more of the atoms in
their topology file is not defined, causing a fatal error.
If you change inp to inp=1 and radiopt to radiopt=0 in your MM/PBSA input
file, hopefully that fixes your problem. Changing the MMPBSA.py from
AmberTools 1.5 will make that change automatically for you (since that used
to be the default).
Another thing to point out from past emails is that the suggestion has been
made, numerous times, _not_ to use this script as a black box.
Understanding what is happening 'behind the scenes' will help debug these
problems.
While there's nothing wrong with using MMPBSA.py from AmberTools 1.5, our
response when people are having trouble with it is "use AmberTools 12" ;).
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Feb 11 2013 - 03:30:03 PST
