On Mon, Nov 9, 2020 at 2:22 PM MYRIAN TORRES RICO <myriam.torres.iiq.csic.es>
wrote:
> 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 - 01:30:02 PST
