On Tue, Aug 20, 2019, Sadaf Rani wrote:
>I am running equilibration of protein-ligand complex system
>vlimit exceeded for step 0; vmax = 1751.7001
This implies that your starting structure has bad forces, even at the
first step. Have you run a minimization before this?
You can also use the checkValidity action (in parmed) or the
checkStructure action (in cpptraj) to look for common problems.
>
> Coordinate resetting cannot be accomplished,
> deviation is too large
> iter_cnt, my_bond_idx, i and j are : 1 24 7053 7052
Atoms 7053 and 7052 are (at least) one place where there are problems.
You could look at these areas (say with a visualization program) to see
if you can spot the problem. But somehow, you need a better starting
structure. Minimization will usually, but not always, provide this.
....dac
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Received on Tue Aug 20 2019 - 19:30:02 PDT
