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 Fri Nov 06 2020 - 08:30:03 PST
