Dear Dr. Case and Dr. Wang,
I'm using antechamber to do atom/bond typing for some ligands from the
pdb, which I have protonated correctly, and in several particular
cases I'm not getting the correct bond/atom types (i.e., rings are
being assigned to be aromatic which should not be).
I can of course provide input files if you're interested in looking in
to this, but I was wondering if you could also help me with
work-arounds.
In particular, if, for example, I use antechamber to generate a mol2
file, and then manually edit the bond types and feed it back into
antechamber again, if I use a suitable -j option, is there a way to
get it to judge only the atom types again, and use the bond types I
have manually provided? Or is there a way to edit one of the
ANTECHAMBER_* files to correct the bond/atom type assignment?
If not, do you have any other suggestions on how to work around this?
Thanks,
David
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Received on Wed Aug 09 2006 - 06:07:08 PDT
