AMBER Archive (2005)

Subject: AMBER: strange case

From: quch 2004 (quch2004_at_yahoo.com)
Date: Wed Sep 14 2005 - 16:57:28 CDT

Hi,
I am trying to run sander for a protein with a
co-valently bonded ligand. The minimization went well,
but the equilibrium (constant volume) keep failed. A
run under constant pressure has failed too. I also
change the tempetarure, rebuild the system, different
minimization, All failed similarly. It looks like the
bond energy was increased somehow and caused the crash
(attachment). The force parameters were prepared from
antechamber. The structure from the minimization looks
good. PDBs from the first a few steps in the
trajectories showd that the ions (Cl-) are moving away
the protein, and the protein structure has change too.

Could anyone give suggestion about how should I
correct this problem?

Thanks,

Jianxin

------------------------------------------------------------------------------
 
 vlimit exceeded for step 7 ; vmax =
20.7171885860067
 
 NSTEP = 8 TIME(PS) = 0.016 TEMP(K) =
  75.36 PRESS = 0.0
 Etot = -162362.2950 EKtot = 9483.4829
EPtot = -171845.7778
 BOND = 34162.1098 ANGLE = 0.0000
DIHED = 0.0000
 1-4 NB = 0.0000 1-4 EEL = 0.0000
VDWAALS = 13408.8673
 EELEC = -219416.7549 EHBOND = 0.0000
RESTRAINT = 0.0000
 Ewald error estimate: 0.2130E+00

------------------------------------------------------------------------------
 
 vlimit exceeded for step 8 ; vmax =
63.3054234360998
 
 NSTEP = 9 TIME(PS) = 0.018 TEMP(K) =
 350.74 PRESS = 0.0
 Etot = 9835.9855 EKtot = 44135.4454
EPtot = -34299.4600
 BOND = 170195.2763 ANGLE = 0.0000
DIHED = 0.0000
 1-4 NB = 0.0000 1-4 EEL = 0.0000
VDWAALS = 13423.7747
 EELEC = -217918.5110 EHBOND = 0.0000
RESTRAINT = 0.0000
 Ewald error estimate: 0.2144E+00

------------------------------------------------------------------------------
 
 vlimit exceeded for step 9 ; vmax =
51.7316467221349
 
 NSTEP = 10 TIME(PS) = 0.020 TEMP(K) =
1736.77 PRESS = 0.0
 Etot = 1084789.0736 EKtot = 218549.5255
EPtot = 866239.5481
 BOND = 1083015.8558 ANGLE = 0.0000
DIHED = 0.0000
 1-4 NB = 0.0000 1-4 EEL = 0.0000
VDWAALS = 13530.5184
 EELEC = -230306.8261 EHBOND = 0.0000
RESTRAINT = 0.0000
 Ewald error estimate: 0.2030E+00

                
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