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 - 04:00:02 PST
