> 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
>
> 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,
Your value of taup is much smaller than I would ever use. Consider using a value 10--50 times larger. Also try a smaller value for cut (say, 10.0), and a smaller value for dt (say 0.001).
....dac
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Received on Mon Apr 18 2011 - 15:00:03 PDT
