Hi Anselm,
I'm bearing in mind your answers, thanks you so much. I found that the
disulphide bond was broken in the docking process, and hence I didn't
defined in my simulation.
Regards
Myriam
"Dr. Anselm Horn" <anselm.horn.fau.de> escribió:
> Hi Myriam,
>
> just to sum up:
> Your first problem was that you forgot to define the disulfide bond, and
> thus your simulation ran with two cystein residues lacking that bond.
> => You have to re-run your simulations.
>
> Your second problem is that your system shows a change in secondary
> structure during the course of simulation. This is by no means strange,
> but reflects the ability of MD simulations to describe the system - but
> can also be an artifact due to the forcefield used.
>
> Good examples for peptide systems exhibiting a change in secondary
> structure are simulations describiting ab-initio folding of peptides.
>
> Also be aware that your visualization program normally decides according
> to the backbone angle topology, what secondary structure the system is
> depicted in. So, small changes here might change the style.
>
>
> Regards
>
> Anselm
>
>
> On 11/06/2020 01:39 PM, MYRIAN TORRES RICO wrote:
>>
>> Hi Carlos,
>>
>>
>> Sorry, I'm not explaining myself well, my problem is one of two
>> sheets has lost the structure... 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
>>
>>
>> Carlos Simmerling <carlos.simmerling.gmail.com> escribió:
>>
>>> Did you define the disulfide bond specifically in leap with a bond command
>>> when you built your system?
>>>
>>> On Fri, Nov 6, 2020, 6:50 AM Dr. Anselm Horn <anselm.horn.fau.de> wrote:
>>>
>>>> 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 Mon Nov 09 2020 - 01:00:03 PST
