No the added portion is not equilibrated, after minimising and heating the
whole protein i applied the restraint on the added portion of protein.
On Thu, Oct 7, 2010 at 4:24 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> did you equilibrate the added portion before letting the rest move?
>
> On Wed, Oct 6, 2010 at 9:56 PM, shweta <swdata7.gmail.com> wrote:
>
> > Hi all,
> > In my target protein (1-338) two residues (286,287) were missing.I added
> > them using modeller and trying to perform 1ns MD on it. But the problem
> was
> > after heating, during equilibration state helix of protein from 286-338
> is
> > getting converted to loop, which results in increase of RMSD as time
> > proceeds. I tried to perform the equilibration and further production run
> > by
> > applying constraint from 286-338, as these portion is away from active
> > site.
> > Is this correct way, or can i do it in better way.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Oct 07 2010 - 08:00:03 PDT
