Dear all.
I am using AMBER 9 and tried simulating a protein molecule with the
ligand and the water free to move while the protein was frozen using
IBELLY.
For this i took the solvated complex and minimized it with DRMS=0.001, which
went well and then i took the Min.rst file and started the simulation using
IBELLY to freeze the protein and allowing the rest to move. The problem is
that after some time (10^5 steps) there is this NAN and vlimit exceeded
error that starts coming inthe output file for the MD. and finally
sander exits. I have read some mails in the reflector about IBELLY and
NAN errors
but i wasn't able to pindown the reason for this behaviour..
I am attaching the output file. There appeared no reason to me that after a
minimization also there can be vdWaals errors. Please help me.
*for a quick look here is the input file for MD..*
&cntrl
ntx = 1, irest = 0,
ntpr = 10, ntwx = 1000, ntwr = 1000,
ntf = 2, ntc = 2, tol = 0.000001,
cut = 8.0,
nstlim = 1000000, dt = 0.001,
nscm = 1000,
iwrap = 1,
ntt = 3, gamma_ln = 1,
ibelly = 1, bellymask = '! :1-948',
lastist = 4000000,
lastrst = 5000000,
/
*and the output when it exits with **error **is.*
NSTEP = 113700 TIME(PS) = 113.700 TEMP(K) = NAN PRESS = 0.0
Etot = NAN EKtot = NAN EPtot = NAN
BOND = 88378.6745 ANGLE = 1895.2066 DIHED = 14.6272
1-4 NB = 172.5705 1-4 EEL = 871.5472 VDWAALS = 34983015.3897
EELEC = NAN EHBOND = 0.0000 RESTRAINT = 0.0000
Ewald error estimate: NAN
------------------------------------------------------------------------------
NSTEP = 113710 TIME(PS) = 113.710 TEMP(K) = NAN PRESS = 0.0
Etot = NAN EKtot = NAN EPtot = NAN
BOND = 82366.9641 ANGLE = 1644.7961 DIHED = 13.4904
1-4 NB = 36.8591 1-4 EEL = 932.8361 VDWAALS = **************
EELEC = NAN EHBOND = 0.0000 RESTRAINT = 0.0000
Ewald error estimate: NAN
------------------------------------------------------------------------------
NSTEP = 113720 TIME(PS) = 113.720 TEMP(K) = NAN PRESS = 0.0
Etot = NAN EKtot = NAN EPtot = NAN
BOND = 76076.4245 ANGLE = 1835.1739 DIHED = 14.5860
1-4 NB = 2813.2429 1-4 EEL = 918.1872 VDWAALS = NAN
EELEC = NAN EHBOND = 0.0000 RESTRAINT = 0.0000
Ewald error estimate: NAN
------------------------------------------------------------------------------
vlimit exceeded for step 113724; vmax = 24.1084
vlimit exceeded for step 113727; vmax = 20.7770
vlimit exceeded for step 113728; vmax = 25.6877
vlimit exceeded for step 113729; vmax = 25.4377
NSTEP = 113730 TIME(PS) = 113.730 TEMP(K) = NAN PRESS = 0.0
Etot = NAN EKtot = NAN EPtot = NAN
BOND = 109815.3417 ANGLE = 2280.3369 DIHED = 17.8472
1-4 NB = 846.2976 1-4 EEL = 1005.7405 VDWAALS = NAN
EELEC = NAN EHBOND = 0.0000 RESTRAINT = 0.0000
Ewald error estimate: NAN
------------------------------------------------------------------------------
vlimit exceeded for step 113730; vmax = 201.3159
vlimit exceeded for step 113731; vmax = 20.7945
vlimit exceeded for step 113732; vmax = 20.3698
vlimit exceeded for step 113733; vmax = 33.9185
vlimit exceeded for step 113734; vmax = 374.9196
vlimit exceeded for step 113735; vmax = 35.6485
vlimit exceeded for step 113736; vmax = 47.9262
****************
*# this is the minimization input file*
&cntrl
ntx = 1, imin = 1, irest = 0, drms = 0.001,
ntpr = 10, ntwx = 100, ntwr = 1000,
cut = 8.0, maxcyc = 100000, ncyc = 1000,
/
********************************
*And the minimization output is*
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
72982 -3.1541E+05 9.5915E-04 4.2499E-02 H2 18310
BOND = 25551.1419 ANGLE = 1974.2793 DIHED = 8718.5065
VDWAALS = 63388.0457 EEL = -465069.4399 HBOND = 0.0000
1-4 VDW = 2985.5177 1-4 EEL = 47040.8718 RESTRAINT = 0.0000
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Aug 19 2007 - 06:07:35 PDT
