Re: AMBER: sander minimization

From: Qiang Lu <qiangl.uci.edu>
Date: Fri, 29 Aug 2003 14:13:53 -0700

Hi atobak,

Usually that means there is one or more clashes or two atoms over 1-4
are too close to each other. 

-- 
Best regards,
 Qiang                            mailto:qiangl.uci.edu
=================Original message text===============
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
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Received on Fri Aug 29 2003 - 22:53:01 PDT
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