Hi All,
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
The DISANG.RST file appears to be read properly from the out file:
============================================================================
===
RESTRAINTS:
Requested file redirections:
LISTOUT = POUT
DISANG = DISANG.RST
Restraints will be read from file: DISANG.RST
Here are comments from the DISANG input file:
##############################
# NOEs
Number of restraints read = 1224
Done reading weight changes/NMR restraints
============================================================================
===
However, according to the NMR Bond and Torsion energies, the calculation
appears to use only the torsion angle restraints, and does not use the NOE
distance restraints (via Bond energy). The Bond energy is 0 for all NSTEPs,
whereas the Torsion energy varies during the calculation:
============================================================================
===
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
100 -3.9495E+03 3.3093E-01 2.4441E+00 HG13 626
BOND = 40.9416 ANGLE = 96.9320 DIHED =
719.4634
VDWAALS = -425.4122 EEL = -2580.3838 EGB =
-2394.0724
1-4 VDW = 282.7257 1-4 EEL = 283.8118 RESTRAINT =
26.5019
EAMBER = -3975.9940
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.318
============================================================================
===
Is it possible there is something wrong with our sander.MPI binary that does
not allow it to utilize distance restraints?
Thanks,
Doug
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Received on Fri May 21 2010 - 11:00:03 PDT
