you're right I just checked and those files aren't in the SI after all. We
will try to fix that.
In the meantime if anyone is interested in the parameters I have placed
them online at
https://github.com/csimmerling/modified-AA-params
On Thu, Nov 5, 2020 at 6:50 AM Dr. Anselm Horn <anselm.horn.fau.de> wrote:
> Dear Carlos,
>
> > 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
>
> this seems to me a most elegant and minimal-invasive way for parameter
> generation for such systems.
>
> [However, I could not find the parameter and library files in the
> supplementary information or on the website (maybe a local browser
> visualization problem ?); could you provide me with the appropriate
> download location? I'd be happy to have a glance at the parameter files
> - many thanks in advance.]
>
> Best regards,
>
> Anselm
>
>
> >
> > 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
> >>>
> >>>
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Received on Thu Nov 05 2020 - 10:30:02 PST
