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 - 05:00:02 PST
