X-ray vs. MD

From: Anton Guliaev <abguliaev_at_lbl.gov>
Date: Thu 25 Jan 2001 14:28:34 -0800

Dear Amber Users,

I am trying to perform molecular dynamics simulations (1-2ns) on
protein/DNA complex determined by X-ray. The coordinates for the complex
deviates from the starting coordinates, after equilibration, with RMSD
values between 1.5 and 2A. The X-Ray structure, used as a starting for
the MD, was determined with the 1.7A resolution. Is it reasonable to
assume that if the RMSD values equal or less than the resolution of the
X-ray structure, than the conformation produced by MD is essentially the
same as the starting X-ray structure? I would appreciate any feedback --
Anton 


-- 
        ************************************
        * Anton B. Guliaev, Ph.D           *
      _ * Life Sciences Division           * _   
     / )* LBNL, Berkeley CA 94720          *( \
    / / * abguliaev_at_lbl.gov                * \ \
  _( (_ * T: 510-486-5773 F:(510)-486-6488 *  ) )_
 (((\ \)**/ )**************************( \**(/ /)))
 (\\\\ \_/ /                            \ \_/ ////)
  \       /                              \       /
   \    _/                                \_    /
   /   /                                    \   \
  /___/                                      \___\
Received on Thu Jan 25 2001 - 14:28:34 PST
Custom Search