Good morning,
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).
But, I have an organic molecule with a charge of -6. Therefore I have
removed six hydrogens at appropriate places in the molecule (there are
some published papers with the same molecule where those specific
hydrogens were removed in preparation for similar simulations). All
other hydrogens are present.
My question is this: is it still appropriate to use antechamber to
assign charges for this molecule of which I have purposely removed six
hydrogens?
Thanks for your time,
--
Wes Barnett | jbarnet4.tulane.edu
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Received on Sat Aug 24 2013 - 09:00:03 PDT
