Hi Amit,
maybe your parameterization approach is not right.
You need parameters for a modified Cys residue, thus you may want to use
a model peptide for parameterization like ACE-CFN-NME.
For this model peptide, you can derive atomic charges (for one or more
conformations), e.g. via the R.E.D./PyRed server.
Then you have to decide, which forcefield parameter set to use for your
protein system and thus for your CFN. After assigning the atom types for
all atoms in your residue, you may find that some of the necessary
parameters are missing. For those, parameters are to be generated either
by separate computations or by adaption from existing force fields.
There are tutorials on the Amber website about how to parameterize
non-standard amino acids.
Regarding your question, whether you can re-use CFN parameters from
Gromacs for Amber: It depends.
Gromacs and Amber are the program suits. If the published Gromacs
parameters were created for the forcefield you intend to use in Amber,
you can savely use those. If they are for a different force field, they
may merely be used as hint.
Regards,
Anselm
> I am trying to parameterize (get .top and .rst7 files) a protein molecule
> with a non standard amino acid cysteinyl-flavin (CFN). CFN contains a
> covalent bond between C4A of flavin mononucleotide (FMN) and SG of
> Cysteine.
>
> I tried antechamber with no success perhaps due to the following reasons
>
> 1. pdb4amber or reduce is not adding hydrogens to CFN. Although reducing
> other residues in the protein
> 2. cif file is not available for CFN. Although, the cif file is available
> for FMN. So parametrization with antechamber works if I treat CYS (as CYM
> (to not reduce SG)) and FMN as separate in the protein pdb. But, doing so
> breaks the cysteine- FMN covalent bond during minimization. I want to
> retain this bond intact during the simulation. Therefore trying to
> parametrize the protein molecule in which CYS and FMN are treated as one
> residue CYM.
>
> I have also tried restraining CYM and FMN using strong force constants on
> these two, but covalent bond breaks during minimization.
>
> After trying these options I write here to seek help with creating
> parameter files for the protein containing CFN residue in AMBER.
>
> Also, like to mention here that parameters for CFN are built and published
> using GROMACS. Can we use these or modify these to work in amber?
>
> Thank You,
>
> Amit
>
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Received on Wed Oct 28 2020 - 08:00:02 PDT
