On Aug 24, 2013, at 9:44 AM, "Barnett, James W." <jbarnet4.tulane.edu> wrote:
>
> I've read some in the mailing list and manual that pdb files should have
> "all hydrogens" for use with antechamber. I believe this is addressing
> the issue that some protein files don't have all of them when retrieved
> from a database (i.e., antechamber doesn't assume hydrogens are present).
It's hard to understand the above. Antechamber is not ordinarily used for proteins. But it never adds hydrogens so they all need to be there in the input file.
>
> But, I have an organic molecule with a charge of -6. Therefore I have
> removed six hydrogens at appropriate places in the molecule
Is this what you mean: you want the charge to be -6, but you have a structure where the charge is zero? In that case it would be appropriate to remove 6 hydrogens. Be sure to use the -n flag to tell antechamber what net charge to use.
....dac
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Received on Sat Aug 24 2013 - 16:30:02 PDT
