AMBER Archive (2003)

Subject: AMBER: sander minimization

From: atobak_at_eden.rutgers.edu
Date: Fri Aug 29 2003 - 15:39:58 CDT

After running sander for minimization, my job exited immediately and the
results I got were as follows:

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

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

     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 7.3833E+12 4.2282E+12 1.9514E+14 CB 2916

 BOND = 1806.5939 ANGLE = 968.3254 DIHED =
2152.0142
 VDWAALS = ************* EEL = -4905.2935 HBOND =
0.0000
 1-4 VDW = 2963.4476 1-4 EEL = 3316.8798 RESTRAINT =
0.0000
 Frac coord min, max: -193613.234 193634.462
 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
************************************************************

My input file "min_vac.in" is as follows:

********************************
 Vac minimize structure
 &cntrl
   imin=1, maxcyc=1000,
   cut=100.0, dielc=4, igb=0,
********************************

I'm pretty new to Amber7 and sander. Can anyone point me in the right
direction as to why my sander job isn't running properly?

My executable command was:
sander -O -i min_vac.in -c cpx.crd -p cpx.top -o min.out -r cpx.rt

Thanks in advance,
Anne

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu