[gmx-users] parametrization of FAD

Justin A. Lemkul jalemkul at vt.edu
Fri Apr 30 16:35:30 CEST 2010

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.



> Regards,
> Giulia Gonnelli


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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