AMBER Archive (2007)

Subject: AMBER: Minimization

From: Sophie Barbe (sbarbe_at_insa-toulouse.fr)
Date: Wed Mar 28 2007 - 02:36:35 CST

Dear amber users,

At the end of the .out file of a minimization of a G protein-coupled receptor,
there is :

 NSTEP ENERGY RMS GMAX NAME NUMBER
   9000 -3.0586E+07 1.9085E+11 1.3847E+13 O 3817

 BOND = 257.3905 ANGLE = 1156.7512 DIHED = 3996.6454
 VDWAALS = -2575.9535 EEL = ************* HBOND = 0.0000
 1-4 VDW = 1189.3758 1-4 EEL = 12856.2338 RESTRAINT = 0.0000
 Frac coord min, max: -15696926.672801873 15696927.611958483
 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.
 SANDER BOMB in subroutine Routine: map_coords (ew_force.f)
 Atom out of bounds. If a restart has been written,
 restarting should resolve the error

Could you explain me bu some means?

Many thanks by advance

Sophie

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