AMBER Archive (2006)

Subject: AMBER: antechamber bond typing questions

From: David Mobley (dmobley_at_gmail.com)
Date: Mon Aug 07 2006 - 15:14:42 CDT

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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