AMBER Archive (2007)

Subject: AMBER: minimization using fcap

From: Syed Tarique Moin (tarisyed_at_yahoo.com)
Date: Wed Jan 24 2007 - 03:08:40 CST


Hello,

I want to run Classical Md unsing fcap = 4.5 in the
input file of minimization, the i got following error
and sander crash down.

I want assistance to fix this problem,

Thanks in advance

4. RESULTS
--------------------------------------------------------------------------------

 ---------------------------------------------------

     eedmeth=4: Setting switch to one everywhere

 ---------------------------------------------------
| Local SIZE OF NONBOND LIST = 4305667
| TOTAL SIZE OF NONBOND LIST = 4305667

   NSTEP ENERGY RMS GMAX
    NAME NUMBER
      1 -nan -nan nan
    H2 3144

 BOND = 1924.2207 ANGLE = 189.2068
DIHED = 14.8045
 VDWAALS = -nan EEL = inf
HBOND = 0.0000
 1-4 VDW = 452.4711 1-4 EEL = -30.6622
RESTRAINT = 0.0000
 Frac coord min, max: -nan
               -nan
 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

Syed Tarique Moin,
Junior Research Fellow,
H.E.J. Research Institute of Chemistry,
International Center for Chemical and Biological Sciences,
University of Karachi, Karachi-75720, Pakistan

tarisyed_at_yahoo.com
tarisyed_at_hotmail.com

 
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