Dear Jason,
Thank you for your reply, I want to simulate separate simulations in 0.5
intervals. I tried to use H++ server for oligomer pdb structure. I have got
FAILURE caused by multiple chains. I could not fix this error. I thought
that if I use H++ server for single chain and I find out which each amino
acid's ionization state and then I use the ionization state to the multiple
chains. Is it possible?
Best regards,
Batsaikhan
On Mon, Jan 4, 2016 at 7:02 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Mon, Jan 4, 2016 at 5:19 AM, Mijiddorj Batsaikhan <
> b.mijiddorj.gmail.com>
> wrote:
>
> > Dear all,
> >
> > Hello, I want to make pH dependent simulation of dimer, trimer and
> pentamer
> > structure of a peptide. How to make it?
> >
>
> The two general approaches are to fix protonation states appropriate for
> each pH you want to simulate and run separate simulations or to use
> constant pH molecular dynamics where the protonation states can change as a
> function of pH.
>
> Which one you should choose depends on what you are trying to learn and the
> nature of your system. It may be worth trying both.
>
>
> >
> > Can I use H++ server for oligomers?
> >
>
> I believe so. Have you tried it? Do the results seem reasonable?
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Tue Jan 05 2016 - 01:00:03 PST
