Dear Amber user
I am using a script file to do an annealing procedure for polypeptides in the
gas phase. I build these peptides using Xleap (saveamberparm...) and generate
the initial.crd and prm.top files to do the annealing procedure. The initial
coordinates of the molecule do not seem to be too close in space. The script
first minmises the seed structure and then goes through annealing cycles; i.e.
increasing T to 800 K and controlled cooling to 0 K to generate seed structure
for next cycle. So far I have never had problems using this procedure, however,
for this peptide the simulation seems to blow up every time.
here is the sander input file:
Amber7 sander dynamics
&cntrl
nstlim = 30000, temp0 = 800, ntx = 1,
ntc = 2, ntf = 2, ntt = 1, ntb = 0, ntpr = 1000
&end
and here is a selected portion of the output file, where things seem to be
getting out of hand:
NSTEP = 11000 TIME(PS) = 11.000 TEMP(K) = 758.52 PRESS = 0.0
Etot = 122.1458 EKtot = 280.3641 EPtot = -158.2183
BOND = 67.5376 ANGLE = 218.8686 DIHED = 114.7998
1-4 NB = 35.9790 1-4 EEL = -130.7328 VDWAALS = -33.7975
EELEC = -430.8731 EHBOND = 0.0000 RESTRAINT = 0.0000
------------------------------------------------------------------------------
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
Translational and rotational motion removed
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
NSTEP = 12000 TIME(PS) = 12.000 TEMP(K) = 812.18 PRESS = 0.0
Etot = 132.9506 EKtot = 300.1948 EPtot = -167.2443
BOND = 91.8496 ANGLE = 195.0248 DIHED = 96.7288
1-4 NB = 32.9253 1-4 EEL = -171.0232 VDWAALS = -26.0068
EELEC = -386.7429 EHBOND = 0.0000 RESTRAINT = 0.0000
------------------------------------------------------------------------------
vlimit exceeded for step 12207 ; vmax = 64.805378984131579
vlimit exceeded for step 12208 ; vmax = 89.849276997277613
at the end of the message, the following appears:
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 3 63 145 146
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
Hope that is enough information. Please advise.
Nick
Nick Polfer
School of Chemistry
West Mains Road
Edinburgh EH9 3JJ
United Kingdom
++44 131 651 3039
++44 131 651 3048 (fax)
Received on Thu Apr 24 2003 - 20:53:01 PDT
