Perfect - many thanks for providing the files.
Regards,
Anselm
On 11/05/2020 07:04 PM, Carlos Simmerling wrote:
> 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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>>>>>
>>>>
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Received on Fri Nov 06 2020 - 02:30:02 PST
