[gmx-users] parametrization of FAD
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.
> Justin A. Lemkul wrote:
>> Giulia Gonnelli wrote:
>>> 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.
>>> Giulia Gonnelli
Dr Thomas Piggot
University of Southampton, UK.
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