[AMBER] Frequency analysis of small molecule, constructing heterocyclic ring systems

From: Dean Cuebas <deancuebas.missouristate.edu>
Date: Tue, 21 Jun 2011 23:07:28 -0500

Dear all,

Two questions:

1) I would like some advice for doing ir frequency analysis for
fine-tuning small molecule parameters in Amber ff10. I see that there are
a few options, and I've never done frequency analysis.

2) In addition, I have some questions as to constructing some planar
aromatic heterocyclics. I find in some cases that the canonical bond
angles reported by gaff can vary as much as 20 degrees from the angles
that are present if one manually constructs the compound with the
canonical bond lengths in gaff. In other words, the "assumed more
accurate, more highly sampled" bond lengths in gaff imply a unique set of
bond angles in a planar system, which can be very far from the canonical
bond angles listed in gaff. Does one keep the gaff bond angle suggestions,
or should the bond angles for the particular atom types be changed in the
frcmod to reflect the "true" set of unique angles that are constructed
from the canonical bond lengths? If one keeps the canonical bond angles
that are significantly off, then the internal energy would be higher than
"normal" given the bond lengths. What is the best way to handle this?

Thanks in advance.

Dr. Dean Cuebas, Associate Prof of Chemistry
deancuebas.missouristate.edu, Ph 417-836-8567 FAX 417-836-5507
Dept. of Chemistry, Missouri State University
Springfield, Missouri 65897

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Received on Tue Jun 21 2011 - 21:30:03 PDT
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