[gmx-users] parametrization of FAD

Thomas Piggot t.piggot at soton.ac.uk
Fri Apr 30 17:07:37 CEST 2010

I should also say that there are parameters for FADH(-) available for 
use with the amber forcefields:



Thomas Piggot wrote:
> 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.
> Cheers
> Tom
> 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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