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).
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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