Thanx a lot to both Carlos and Deepangi, By the way my protein consists of
20 model structures with RMSD of 0.5 A between them. So hope I can chose any
of the structure to start my simulation.
On Wed, Mar 10, 2010 at 1:45 PM, Deepangi Pandit <dnp5.njit.edu> wrote:
> Hi Nicholus:
> It is clear from Dr. Simmerling's reply that you should simulate more
> than one protein structure. I just want to share my thoughts on how to
> choose NMR structures from the all models given in the pdb file. Here
> are the options
>
> 1. You can calculate RMSD of structures after superimposing structures
> on backbone atoms of the rigid part(info about the rigid part may be
> available from the corresponding published paper). This will give you
> a range of values
>
> 2. Divide this range in reasonable bins then select a structure from each
> bin
>
> All the best!
> Deepa
>
>
>
>
>
> On Wed, Mar 10, 2010 at 6:37 AM, Carlos Simmerling
> <carlos.simmerling.gmail.com> wrote:
> > my opinion is that you should simulate more than 1 (for example, choose 2
> > and simulate both), and your conclusions should be the same from both
> > simulations. if the conclusions depend on which model is chosen, this
> > represents uncertainty.
> >
> > On Wed, Mar 10, 2010 at 4:50 AM, nicholus bhattacharjee <
> > nicholusbhattacharjee.gmail.com> wrote:
> >
> >> Dear community,
> >> I want to simulate a protein whose structure is
> >> elucidated with NMR. As we know there are number of models in the NMR
> >> structure PDB file, I am confused which one to chose. Please help.
> >>
> >> --
> >> Nicholus Bhattacharjee
> >> PhD Scholar
> >> Department of Chemistry
> >> University of Delhi
> >> Delhi-110007 (INDIA)
> >> Phone: 9873098743(M)
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> >>
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--
Nicholus Bhattacharjee
PhD Scholar
Department of Chemistry
University of Delhi
Delhi-110007 (INDIA)
Phone: 9873098743(M)
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Received on Thu Mar 11 2010 - 03:30:03 PST
