Hi Anselm,
Sorry, I'm not explaining myself well, effectively it has not really
disappeared, but the structure of the sheet does not exist ... and it
had not happened to me until now. Can a molecular dynamic cause this
phenomenon in protein? lose the structure of one of the sheets?
Thanks in advance,
Myriam
"Dr. Anselm Horn" <anselm.horn.fau.de> escribió:
> Hi Myriam,
>
> I'm sorry but I do not understand your second problem:
> One of the domains in your protein has "disappeared"? What do you mean
> by that?
> In your screenshots, I can spot a single protein chain with two (more or
> less structured) regions and a ligand system in sticks, but nothing
> "disappeared" here. The structure of sheet structure on the left side is
> lost in one pic, but the protein is still there...
>
> Regards
>
> Anselm
>
>
> On 11/06/2020 12:21 PM, MYRIAN TORRES RICO wrote:
>> Hi Bill,
>>
>> I rectify with my previous message, sorry. I have checked just that,
>> and indeed my disulfide bond was not defined, and that's why it
>> appeared broken in all dynamics. So my problem is summarized in: Even
>> not having put this bond in my input ... because in some cases one of
>> the two domains of the protein disappears? I am attaching two images
>> so you can see it better. I have opened the final molecule with
>> several programs and only one of two domains appears...
>>
>> Thanks in advance,
>>
>>
>> Myriam
>>
>>
>>
>>
>>
>> Bill Ross <ross.cgl.ucsf.edu> escribió:
>>
>>> Normally bonds that seem to disappear were not made in the first place.
>>>
>>> Bill
>>>
>>>
>>> On 11/6/20 2:45 AM, MYRIAN TORRES RICO wrote:
>>>> Dear all,
>>>>
>>>> I wanted to take a query about some results that I have obtained in my
>>>> molecular dynamics.
>>>> I have launched a dynamic of a protein-ligand complex (the ligand is a
>>>> tretasaccharide), and of the two domains that the pdb of my protein
>>>> initially presents, the disulfide bonds that form one of them ends up
>>>> breaking ... But the energy data endings are the same as in any other
>>>> dynamic that has been launched under the same conditions and with the
>>>> same complex ...
>>>> Has someone this or something similar happened to him?
>>>> any ideas?
>>>>
>>>> Thanks in advance,
>>>>
>>>> Myriam
>>>>
>>>>
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Received on Fri Nov 06 2020 - 04:30:02 PST
