On Mon, Dec 12, 2016, Andreas Tosstorff wrote:
>
> I am trying to prepare a ligand with antechamber. The job fails and
> acdoctor states:
>
> "Warning: There are no hydrogen and halogens in this molecule, it is
> highly possible that this molecule has open valence"
I cannot reproduce your result: acdoctor doesn't report any errors for me.
And antehcamber works fine, giving atom types that look fine, and not having
troubles with hydrogens. Please double check that no "operator error" is
involved here, i.e. that you are loading the file you intended to load.
Examine any AC* files that are created.
Which version of AmberTools are you using? Try AmberTools16 if you are not
already doing so (although I don't see why that should make a difference.)
If you still can't figure it out, post your input pdb as an attachment:
putting in in-line in emails often causes it to get mangled.
Also, indicate which OS and compiler you are using.
....dac
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Received on Mon Dec 12 2016 - 08:30:03 PST
