AMBER Archive (2009)

Subject: Re: [AMBER] Re: antechamber am1-bcc issues

From: case (case_at_biomaps.rutgers.edu)
Date: Sat Aug 08 2009 - 14:20:44 CDT

On Sat, Aug 08, 2009, gilbert_at_bluemarble.net wrote:
>
> The problem is not in the AM1 charges or the bond correction
> parameters but in the assignment of the bond types for the nitro group.

Kevin:

Thanks very much for the quick analysis!

> It would be most useful to have a suite of molecules with assigned
> atom and bond types that correspond to the test suite used by Bayley et
> al in parameterizing the AM1BCC method. I wrote an email to the list
> last month pointing out that Antechamber did not reproduce the structure
> given in the Bayley paper (which is the only case I know of) and I have
> not had any response to that email.

I apologize for letting this slip. Junmei has been out of email contact for a
while (I suspect some emails may have been going to a mailbox he is no longer
reading), and I've swamped with travel. But we do have your emails archived,
and I will try to address the problems you raise as soon as I can.

I agree about the need for a suite of molecules to serve as test cases. If
you (or anyone else reading this) has a good suggestion for implementing this,
I'm willing to help with the Amber part.

Again, I apologize for the delays in dealing with mail-list posts about
am1-bcc issues.

...regards...dac

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