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 - 04:30:03 PST
