AMBER Archive (2009)

Subject: [AMBER] problem with the energetics of the system

From: Mahmoud A. A. Ibrahim (m.ibrahim1982_at_yahoo.com)
Date: Sat Jul 11 2009 - 18:23:13 CDT

Dear AMBER
When I do restrain on my protein residue during heating step it gives me the following error:
NSTEP =        0   TIME(PS) =       0.000  TEMP(K) =     0.00  PRESS =     0.0
 Etot   =   -134725.7151  EKtot   =         0.0000  EPtot      =   -134725.7151
 BOND   =        85.3347  ANGLE   =       432.0654  DIHED      =      1538.9900
 1-4 NB =       566.6409  1-4 EEL =      7559.2252  VDWAALS    =     22730.5512
 EELEC  =   -167638.5224  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 Ewald error estimate:   0.9061E-04
 ------------------------------------------------------------------------------

vlimit exceeded for step      4; vmax =    20.9556

     Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are :    0    2 1286 2654 2660

     Note: This is usually a symptom of some deeper
     problem with the energetics of the system.
--------------------------
This is my input file:
Heating Step of MMP3 (MMMM): stage-1
 &cntrl
  imin= 0,
  irest=0,
  NTX=1,
  ntb= 1,
  NTPR=500,
  NTWX=500,
  NTWR=500,
  ntr=1,
  Tempi=00.0,
  Temp0=50.0,
  NTT=3,
  gamma_ln=1.0,
  NTC=2,
  NTF=2,
  cut= 12.0,
  nstlim=2500,
  dt=0.002
 /
Keep Protein and inhibitor fixed with weak restraints
10.0
RES 1 177
END
END
--------
Also, I decreased my restrain to 5, and I got the same error.
Any suggestions would welcome;
Thanks in advacne;
Sincerely;
M. Ibrahim

      
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