recently, I encountered an error at the beginning of the simulation, which related to Atom 3662,
please let me know the solution of this error:
FATAL ERROR: Atom 3662 has bad hydrogen group size. Check for duplicate bonds...
by the way, I didn't find a duplicate bond in the parameter file and I want to know, what's the meaning of hydrogen group size?
is it possible to know the root of this message?
best regards,
soroush
It may be helpful to include the coordinate file for inspection. With just what you've said, ensure you don't have alternative conformations on the residue to which atom 3662 belongs. Some crystallographic refinement programs will output just hydrogens in alternative positions, so e.g. there may be 2 HD1 hydrogens on that residue and HD1 in A conformation is involved in an H-bond and HD1 in B conformation involved in a different H-bond, giving you a bad group size.
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