you may find it useful to look at the methods in our recent article where
we parameterized a flavin bound to Cys. We did not change the Cys since it
already is intended to form a bond (using Cyx).
Unraveling the Mechanism of a LOV Domain Optogenetic Sensor: A Glutamine
Lever Induces Unfolding of the Jα Helix
ACS Chem. Biol. 2020, 15, 10, 2752–2765
https://pubs.acs.org/doi/10.1021/acschembio.0c00543
On Wed, Nov 4, 2020 at 11:23 AM Amit Sharma (Asstt. Prof., MCARS) <
asharma4.jmi.ac.in> wrote:
> Thank You David,
>
> Can you also guide about how to generate .lib or .mol2 file for CFN because
> CFN is a non standard cysteine residue.
>
> CFN is built through a covalent bond bstween SG of CYM (cysteine with non
> reducable SG) and C4A carbon of flavin mononucleotide (FMN). Amber could
> help generate lib or mol2 files for FMN because its FMN.cif is available in
> pdb database. But, how to deal with CFN (or how to get its .cif) is giving
> tough time to me.
>
> Best,
>
> Amit
>
> On Wed, 4 Nov 2020, 18:46 David A Case, <david.case.rutgers.edu> wrote:
>
> > On Wed, Nov 04, 2020, Amit Sharma (Asstt. Prof., MCARS) wrote:
> > >
> > >> source leaprc.protein.ff14SB
> > >> source leaprc.gaff
> > >> com = loadpdb CFN.pdb
> > >> chig = sequence { ACE com NME }
> >
> > Above is incomplete. You need to load the CFN residue by using a command
> > like "loadOff CFN.lib" or "CFN = loadMol2 CFN.mol2" After one of these
> > commands, type "list" to be sure that you have a CFN unit loaded, and
> > use the "desc" command to look at what is inside it, especially at the
> > head and tail properties. Compare the description of CFN to what you
> > get for ALA (say), to see what an amino acid unit is supposed to look
> > like.
> >
> > Then your sequence command would look like "sequence { ACE CFN NME }"
> >
> > ...hope this helps....dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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Received on Wed Nov 04 2020 - 09:00:02 PST
