[gmx-users] Re: FAD co-factor minimizaiton

Anton Feenstra 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) *
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam   |
|(   |   )| | | De Boelelaan 1083 - 1081A HV Amsterdam - Netherlands  |
| \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P440 |
|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
|             | "If You See Me Getting High, Knock Me Down" (RHCP)    |

More information about the gromacs.org_gmx-users mailing list