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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 21 2010 - 12:00:03 PDT
