[gmx-users] parametrization of FAD

Thomas Piggot t.piggot at soton.ac.uk
Fri Apr 30 16:54:44 CEST 2010

FAD has been prameterised previously. IIRC the parameters are in the 
appendix of the thesis of Anton Feenstra. Try googling for him and you 
should find it.



Justin A. Lemkul wrote:
> Giulia Gonnelli wrote:
>> Hello,
>> my name is Giulia Gonnelli and i'm a new user of the software Gromacs. 
>> I'm performing an energy minimmization of several proteins containig 
>> biological cofactors.
>> I have problems with the cofactor FAD which has not been parametrized 
>> yet on the gromos forcefields. I was wondering how to add new parameters 
>> fon unrecognised molecules in Gromacs. I found in literature that 
>> actually there are some parameters for the FAD cofactor but i don't know 
>> how and where do i have to add these parameters. I'm not used to use 
>> gromacs so i apologyze for my simple question...and my english too.Thanks.
> All the necessary components for a reasonable start at an FAD topology are 
> certainly part of the Gromos force fields.  The FMN moiety is described in the 
> .rtp file, as well as ATP, which could be used for the other nucleotide.  You 
> can piece the topology together from there.  I have found that most functional 
> groups are quite transferable between different species in the Gromos parameter 
> sets.  So, theoretically, you could write an .rtp entry for FAD and have pdb2gmx 
> build it automatically into your topology.
> If you have a complete FAD topology that you trust, you can build an .itp file 
> for it.  The manual (Chapter 5) is your friend here.
> Be aware that parameterization in general is a very advanced concept, so if you 
> are going to be dealing with any other cofactors besides FAD, your life will get 
> complicated.  Deriving new parameters is a task only suited for experienced 
> users who plan to devote a substantial amount of time (read: weeks or months) to 
> just deriving suitable parameters.  The piecemeal approach I describe for FAD 
> seems to work pretty well, but may not always be possible or feasible.
> http://www.gromacs.org/Documentation/How-tos/Parameterization
> -Justin
>> Regards,
>> Giulia Gonnelli

Dr Thomas Piggot
University of Southampton, UK.

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