[gmx-users] Re: FAD co-factor minimizaiton
feenstra at few.vu.nl
Mon Jan 2 10:05:41 CET 2006
tprakci at ttnet.net.tr wrote:
> Hello Feenstra,
> I am working on MAO enzyme which contains FAD as co-factor. I would like to get your contribution. I edited the gromacs ffgmx.rtp and ffgmxbon.itp files for lacking parameters. Although how good they have been is questionable. When I perform EM on the FAD alone in the vacuum, the resultant structure shows that some bonds got broken.
> Could you give any idea for this? Thanks.
Something that looks like bonds breaking during EM in vacuum is almost
certainly due to an error in your topology and/or forcefield parameters.
Which topology did you use to start? IIRC, there is no FAD in the ffgmx,
only FMN (in different redox states) and adenine separately.
Since you are apparently just starting out, I would suggest using the
Gromos (ffG43a1) forcefield instead, or one of the newer ones (e.g.
53a6) with improved parameters for nucleic acids. I'm not sure if FMN
is still in there, if not you'd have to assign the proper parameters for
the flavin. You may want to check them anyway, since they may not be
consistent with the other nucleotides anymore. Also, I'd recommend
sending your questions (also) to the Gromacs user list (you have to
subscribe first at www.gromacs.org), there are more people working on
* NOTE: New Affiliation, Phone & Fax numbers (below) *
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| _ _ ___,| K. Anton Feenstra |
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