[gmx-users] help with FAD topology, please

Justin A. Lemkul jalemkul at vt.edu
Sun Mar 1 17:53:14 CET 2009

Miguel Quiliano Meza wrote:
> Dear all.
> I am a new user of GROMACS, I have read the user book and free tutorials 
> in the WEB, but now when I try to do a simulation, appears FAD no 
> topology, I have been reading that PRODRG server is a way to achieve 
> that goal, I tried but the output format is different, it means old 
> version (for gromos 96 forcefield).

PRODRG will give ffgmx-compatible output, but PRODRG beta will give 
Gromos96-compatible output.  The latter is preferred, but in either case you 
will have to manually alter the topology.

> I do not mind edit by hand (I want to learn), I searched in the 
> gmx-users but no one shares the  FAD topology. Until now, I can't run my 
> simulation.

In the .rtp file of several Gromos96 force fields you will find a few different 
FMN variants.  This should provide you with a reasonable starting point for 
creating your FAD topology (when you consider that ATP is also part of the force 
field as well).


> So, I would be very grateful if someone could give me "tips", advices or 
> the FAD topology (in this way I could see my errors).
> Thanks in advance.
> Miguel.
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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