In this case, Iım pretty sure my restraint energies should not be 0.
I also performed a serial simulation (Amber 10, sander) and see similar
results (Bond = 0).
I think it could be something wrong with these specific Amber10
sander/sander.MPI binaries, as calculations on a different computing cluster
(Amber 10 binaries, but compiled a while ago) reports restraint energies >
0. We only have Amber 10 bug fixes 1-32 for the problematic binaries, and
the current is 35. Bugfixes 1-17 were applied to the older binary that
reports restraint energies > 0.
I havenıt this specific dataset on the older binaries (yet), but I noticed
this problem (Bond = 0) previously on another dataset, switched to another
cluster running Amber 10 (an older complied version), and the calculations
gave results with Bond > 0.
I suppose we should recompile and hope for the best ...
Thanks,
Doug
On 5/21/10 2:19 PM, "case" <case.biomaps.rutgers.edu> wrote:
> On Fri, May 21, 2010, Douglas Kojetin wrote:
>> >
>> > I am trying to perform protein structure refinement using AMBER 10
>> > (sander.MPI). My input restraint file (DISANG.RST) contains 888 NMR NOE
>> > distance restraints and 336 torsion angle restraints (84 dihedral angles,
>> > 252 chirality restraints). The total number of restraints = 1224.
>> >
>> > The full output file is attached
>
> Specific advice:
> It is probably the case that all your restraint energies are zero. The
> summary printed at the end only prints restraints whose energy is greater than
> pencut (I think that is the name), which defaults to some positive value.
> Set pencut=-1.0 (or any negative number) to see all of the restraints in the
> summary at the end.
>
> General advice:
> Try a serial simulation, to eliminate the possibility of specific parallel
> problems. Don't run a many-step simulation with a thousand restraints: set up
> a 10 step run (with ntpr=1) and use a single restraint. The command
> "LISTIN=POUT" is also useful in seeing how sander is interpreting your input.
>
> ....dac
>
>
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Received on Fri May 21 2010 - 12:00:04 PDT
