On Fri, Jun 16, 2017, Ashish Radadiya wrote:
>
> No main problem starts from here actually. I think either of antechamber
> code has problem/bug. Because, even after manually editing 'ac' file
> gives same error warning in prepi generation as below:
>
> Warning: ATOM N2 has unfilled valence, assuming the linked atom name (in other residue) is "M"
It's not clear whether you expect the ligand to be covalently linked to
other residues, or whether the ligand is a complete molecule on its own. It
looked to me like it is a complete molecule on its own. If so, just give
antechamber either (a) a pdb file; or (b) a correct mol2 file (that has
correct bond orders).
If you get a message like "unfilled valence", and you cannot figure out why,
please post the pdb file you used, and the exact antechamber command line
you used.
As I said earlier, when I used your *.ac files, things worked fine.
Hand-editing a .ac file is error-prone, so I'd suggest avoiding that. I'm
pretty sure if you use correct inputs to antechamber, you will get correct
outputs.
....dac
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Received on Sun Jun 18 2017 - 12:00:02 PDT
