AMBER Archive (2003)

Subject: AMBER: atomic clash or structure size?

From: atobak_at_eden.rutgers.edu
Date: Tue Sep 02 2003 - 16:08:51 CDT

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   4. RESULTS
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     eedmeth=4: Setting switch to one everywhere

 ---------------------------------------------------
| Local SIZE OF NONBOND LIST = 8193242
| TOTAL SIZE OF NONBOND LIST = 8193242

   NSTEP ENERGY RMS GMAX NAME
NUMBER
      1 6.7439E+07 1.7942E+07 1.0385E+09 NZ 2889

 BOND = 216.5081 ANGLE = 905.7987 DIHED =
2173.1263
 VDWAALS = 67435606.3650 EEL = -4909.3228 HBOND =
0.0000
 1-4 VDW = 1417.0613 1-4 EEL = 3308.6923 RESTRAINT =
0.0000

****************************************

 Frac coord min, max: 0.0619183818 1.05405019
 The system has extended beyond
     the extent of the virtual box.
 Restarting sander will recalculate
    a new virtual box with 30 Angstroms
    extra on each side, if there is a
    restart file for this configuration.
 EWALD BOMB in subroutine Routine: map_coords (ew_force.f)
 Atom out of bounds. If a restart has been written,
 restarting should resolve the error

****************************************

The vdwaals energy suggests some type of atomic clash, but the error
message about the virtual box suggests that there is a problem in the
size of the receptor. Which one is it?

Thank you!

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