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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>>>
>>
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Received on Thu Nov 05 2020 - 04:00:02 PST
