Thank you for your suggestions.
I am wondering is it essential for missing amino acid rebuilt before the
long-time MD simulation. In fact, PDB file obtained from PDB.org usually
lose some amino acids. These missing amino acids located at binding sites
should be rebuilded before the perform of MD simulation. However, is it
necessary to rebuild the missing amino acids outside the binding interface
before long timescale MD simulation?
Thank you for your help.
Carlos Simmerling <carlos.simmerling.gmail.com>于2017年9月8日 周五下午10:39写道：
> I think people may not be understanding your question. Try to describe
> exactly what you did and what happened, or maybe get help from someone that
> can help you develop a more clear explanation.
>
> On Sep 8, 2017 10:29 AM, "jacky zhao" <jackyzhao010.gmail.com> wrote:
>
> > opps,
> > No one can answer this question?:)
> >
> >
> >
> > jacky zhao <jackyzhao010.gmail.com>于2017年9月5日 周二下午1:00写道：
> >
> > > Hi everyone
> > > Recently, I have performed protein-protein complex long-time MD
> > > simulation with more than 1µs by Amber. I am wondering that rebuilt the
> > > missing amino acid gap is essential for long-time MD simulation, even
> > > though these missing amino acids were not located at the binding
> > interface?
> > >
> > >
> > > Thank you for taking your time.
> > >
> > >
> > >
> > > --
> > > Lei Zhao, Ph.D.
> > > International Joint Cancer Institute of the Second Military Medical
> > > University
> > > National Engineering Research Center for Antibody Medicine
> > > New Library Building 11th floor,800 Xiang Yin Road
> > > Shanghai 200433
> > > P.R.China
> > >
> > --
> > Lei Zhao, Ph.D.
> > International Joint Cancer Institute of the Second Military Medical
> > University
> > National Engineering Research Center for Antibody Medicine
> > New Library Building 11th floor,800 Xiang Yin Road
> > Shanghai 200433
> > P.R.China
> > _______________________________________________
> > 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
>
--
Lei Zhao, Ph.D.
International Joint Cancer Institute of the Second Military Medical
University
National Engineering Research Center for Antibody Medicine
New Library Building 11th floor,800 Xiang Yin Road
Shanghai 200433
P.R.China
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Received on Sat Sep 09 2017 - 00:30:03 PDT
