On Fri, May 16, 2014, Valentina Romano wrote:
>
> By the way, I ran a minimization and a MD for the ligand itself and the
> protein itself.
OK....forget about all the more complex stuff. You need to solve this problem
first.
>
>
> The difference between the energy's components of the last min step and the first MD step is this:
> min.
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 500 -1.9339E+02 6.1958E-03 1.5149E-02 C4 10
>
> BOND = 1.9919 ANGLE = 10.0103 DIHED = 0.0000
> VDWAALS = -0.8645 EEL = 49.4645 HBOND = 0.0000
> 1-4 VDW = 6.3659 1-4 EEL = -260.3614 RESTRAINT = 0.0000
>
> MD
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 260.00 PRESS = 0.0
> Etot = -183.1726 EKtot = 10.3332 EPtot = -193.5059
> BOND = 1.8793 ANGLE = 10.0103 DIHED = 0.0000
> 1-4 NB = 6.3659 1-4 EEL = -260.3614 VDWAALS = -0.8645
> EELEC = 49.4645 EHBOND = 0.0000 RESTRAINT = 0.0000
>
> In that case the BOND component does not change too much but the MD stopped at the step 2 with the following message:
>
> vlimit exceeded for step 2; vmax = 129.5132
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 1 4 6 14
I think you will have to post your prmtop and coordinate files (after
minimization). But first, look to see what atoms 6 and 14 are -- are they
supposed to be bonded to each other? And, just for sanity sake, re-run
the MD with tempi=0.0 and ntt=0. But it looks like there is something
very wrong with the way your ligand is constructed, but something that
cannot be debugged without seeing the actual files.
....dac
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Received on Fri May 16 2014 - 05:30:03 PDT
