AMBER Archive (2008)
Subject: AMBER: GAFF atom types for flavin (again)
From: Hans Martin Senn (senn_at_chem.gla.ac.uk)
Date: Thu Jan 17 2008 - 14:47:54 CST
I brought up this question a while back, but didn't get any answers.
So I give it another stab...
I'm looking at a quite large organic molecule that has a flavin
(isoalloxazine) moiety in it, like the co-factors FAD or FMN (for a
structure, see <http://www.ebi.ac.uk/msd-srv/msdchem/cgi-bin/cgi.pl?
ION=1>). Eventually I would like to use GAFF for my whole molecule,
including the isoalloxazine ring system.
However, antechamber 1.27 has problems with assigning GAFF atom types
for this case. Especially the two nitrogens in the central ring come
out completely wrong: nf (meant to be in a chain) for N5 and nh
(meant to be an aniline-type N) for N10 (for the numbering see the
above link). When optimized with these parameters, the ring system
actually becomes non-planar...
I was therefore trying to assign the atom types by hand, using the
definitions and examples provided in the GAFF and antechamber papers.
However, I don't think that I have found an unambiguous solution.
Below I'm listing several sets of atom types (again using the same
atom no. antechamber my guess 1 my guess 2
N1 nd nd nd
C2 c c c
N3 n na na
C4 c c c
C4a cc cc cc
N5 nf nd nd
C5a ca ca cd
C6 ca ca ca
C7 ca ca ca
C8 ca ca ca
C9 ca ca ca
C9a ca ca cc
N10 nh na na
C10 cc cc cc
N3: antechamber proposes n (amide N), which seems not unreasonable.
But there is an example in one of the papers where they use na (sp2 N
with 3 substituents) for a similar "conjugated lactam" N. Which one
C4, C4a: OK
N5: nf is certainly wrong. I would opt for nd.
C5a, C9a: Should I treat the all-carbon ring as a benzene ring,
assigning all six carbons as ca; or should the "conjugated ring
motif" N1-C10-C4a-N5 be extended to include C5a and C9a? In the
latter case, they would be cd and cc, respectively.
C6, C7, C8, C9: OK
N10: Obviously, antechamber's nh is incorrect. I would go with na.
I would very much appreciate if the GAFF/antechamber experts could
help me out with this and comment on my choices. Even after studying
the two pertinent papers very carefully, I am not convinced that I
fully understand the GAFF type assignment logic and the criteria that
differentiate one type from another.
Thanks for any replies in advance!
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, fax: +44 141
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