I think you need to be more clear about what you are trying to learn. If the
peptide is not in the crystal structure, do you have reason to believe that
it is not flexible? What is the evidence that the current simulation is
incorrect? What experimental data could you use to help you guide your
system setup/model building?
On Mon, Mar 7, 2011 at 8:57 AM, <asakiayumikio.gmail.com> wrote:
> Dear AMBER members,
>
> Recentl i came across a problem of dealing with flexibility of peptide
> during prod. process.
>
> the simulation is about acetyltransfer to histone peptide.
>
> the original crystal structure does not contain the peptide substrate, i
> model the peptide from the homologous family member, including enzyme,
> peptide but the accoa turn out to be coa. some after some minimization, to
> model seems to be alright.
>
> during prod. process, when i trajin out a pdb file from the .mdcrd file, it
> looks like that the peptide changed a lot.
>
> so i plot the peptide rmsd, i find it turn larger than 2, and has the trend
> to be larger.
>
> I look into the model i get and did find about 6 groups hydrogen and more
> than 30 groups van der Waals interaction between the complexes.
>
> so i am very doubt how can i keep the peptide stable and remain the
> intractions as much as possible during prod.
>
> I try to fix some groups of interaction atoms, i find that the peptide
> still goes flexible and if i get rid of these fixes
>
> after about 0.5ns, the structure i get will be unacceptable.
>
> so, it will be appreciate of anyone of you here to give me some
> suggestions,
>
> thank you very much for you quick answers.!
>
>
> Best regards
>
> asakiayumikio.gmail.com
> 2011-03-07
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Received on Mon Mar 07 2011 - 06:30:16 PST
