Hi all,
I tried to calculate delta G binding between two ligands using soft core
potential. I was able to finish energy minimization for all steps but when
I did equilibration for step2 (the one with soft core turned on) I
encounter such a problem:
'vlimit exceeded for step 1759; vmax = 30.3383
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 0 360 720 721
Note: This is usually a symptom of some deeper
problem with the energetics of the system.'
I checked my coordinates and trajectories and found no close contact or
atom overlap in the coordinates.
My input file is:
' &cntrl
imin = 0, ntx = 1, irest = 0,
ntf = 1, ntc = 2,
ntb = 2, cut = 12.0,
nstlim = 50000, dt = 0.002,
temp0 = 300.0, ntt = 3, gamma_ln = 5,
ntp = 1, pres0 = 1.0, taup = 0.2,
ntpr = 1000, ntwx = 1000, ntwr = 5000,
icfe=1, clambda = 0.1,
ifsc=1,
crgmask=':1.N1,C6,H6,C5,C7,H71,H72,H73,C4,O4,N3,H3,C2,O2',
scmask=':1.N1,C6,H6,C5,C7,H71,H72,H73,C4,O4,N3,H3,C2,O2',
&end'
I set ntf =1 since it is required. I also did a heating up without density
equilibration separately. However, same problem occurred again.
I would like to hear your comments and advice on my problem. Thank you very
much.
Yi An
Graduate student
Department of Chemistry
Texas A&M University
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 18 2011 - 12:30:02 PDT
