AMBER Archive (2007)

Subject: AMBER: GAFF atom typing for flavin

From: Hans Martin Senn (senn_at_chem.gla.ac.uk)
Date: Sat Aug 04 2007 - 11:15:30 CDT

Dear AMBER community

I am using antechamber/leap to generate topologies for largish
organic molecules (up to ~300 atoms) containing a flavin (FAD/FMN/
isoalloxazine) moiety. While this works perfectly for most parts of
the molecules, the automatic atom-type assignment for the
isoalloxazine ring system is completely unreasonable. In particular,
antechamber fails to recognize that the three rings together form an
aromatic system.
So I have been trying to assign the GAFF atom types manually, using
the definitions and examples in the GAFF and antechamber papers.
However, being new to this, I would like to ask for your comments on
whether my choices make sense. Specifically: Should I use cc/cd or
rather ca for the C atoms in the fused bonds? Is na OK for the imide N?

                    o
                    || |
                    c nd ca
                   / \ // \ / \\
               --na cc cd ca--
                  | | || |
               o==c cc cc ca--
                   \ // \ / \ //
                    nd na ca
                           | |

(Sorry for this somewhat awkward drawing... you must use a monospaced
font to view it. Dangling bonds connect to H or alkyl substituents.)

A follow-up question then is: Do I need to adjust the IMPROPER
section in the prepin file manually as well because I turned, e.g.,
pyramidal nh into planar na?

Thanks for any hints!

Best wishes
Hans

.......................................................
Dr. Hans Martin Senn
Lord Kelvin/Adam Smith Research Fellow
University of Glasgow
Department of Chemistry
Joseph Black Building, University Avenue, Glasgow G12 8QQ, Scotland/UK
E-mail: senn_at_chem.gla.ac.uk, phone: +44 141 330 6574

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