On Tue, Jun 28, 2016, bharat gupta wrote:
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 2 392 803 804
Note what usually follows this message: 'Note: This is usually a symptom of
some deeper problem with the energetics of the system.'
It's not really possible to tell a lot more via email. You need to see if the
water in question is interacting with the ligand, and if so, how. You
generally indicate that the problem is with a density equilibration step,
so you might try to increase taup.
>
> So, I looked at the structure as advised by David and found a close contact
> between the water molecule's O and H atoms (803 and 804).
Not sure at what this means: if you are using SHAKE, and if these atoms
are in the same water molecule, they should have a bond distance exactly equal
to the ideal bond distance in whatever water model you chose. Please double
check your identification of atoms 803 and 804: is this a water added by
solvateBox (or similar command), or one in the original PDB file you started
from?
Bottom line: the problem is almost certainly with your system setup and force
field, not with the details of the mdin files you choose to use. You'll have
to experiment: e.g. leave out this one water molecule, and see what happens.
Really do a calculation with ntpr and ntwx set to 1 and visualize the
trajectory in this vicinity right up until the time when the SHAKE error
occurs. Maybe remove the ligand and see if that helps. Try the GAFF force
field for the ligand rather than GLYCAM. etc. You need to somehow
narrow down the possible causes of the problem.
...good luck...dac
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Received on Mon Jun 27 2016 - 19:30:03 PDT
