Anyone who is interested can check this software: MRP.py: A Parametrizer of Post-Translationally Modified Residues (https://pubs.acs.org/doi/abs/10.1021/acs.jcim.0c00472 <https://pubs.acs.org/doi/abs/10.1021/acs.jcim.0c00472>).
Pengfei
> On Nov 6, 2020, at 5:15 AM, Dr. Anselm Horn <anselm.horn.fau.de> wrote:
>
> 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 20 2020 - 08:30:05 PST
