AMBER Archive (2008)

Subject: Re: AMBER: GAFF atom types for flavin (again)

From: Junmei Wang (junmwang_at_gmail.com)
Date: Thu Jan 17 2008 - 23:21:21 CST

Hi, Hans,
Thank you very much for the email. I found a bug in ring.c that causes the
atom type assignment not very correct for your molecule. We will prepare a
bugfix or release the latest version of antechamber.
I also attached the correct assignment generated with the latest
antechamber.

Best

Junmei

On Jan 17, 2008 2:47 PM, Hans Martin Senn <senn_at_chem.gla.ac.uk> wrote:

> Dear all
>
> 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?
> FUNCTION=record&ENTITY=CHEM_COMP&PRIMARYKEY=1510&PARENTINDEX=-1&APPLICAT
> 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
> numbering system):
>
> 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
>
> Comments:
> N1: OK
> C2: OK
> 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
> is right?
> 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.
> C10: OK
>
> 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!
>
> 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, fax: +44 141
> 330 4888
>
>


  • application/octet-stream attachment: FAD.prepi
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