Hello,
I am simulating DNA binding protein on Amber6. This protein moves
its pair of arms very dynamically, and seems to hold DNA.
Question is about the equation<a href=
http://amber.ch.ic.ac.uk/eqn.txt</a>> here.
Is the first part of V uses some approximation? If so, dynamic movement
of my protein would be nonsense?
I read r0 means 'avarage of bond length', but what average? Is it
calculated on every MD or already difined?
I am not familiar with such problems... Suggestions needed to help my
MD from nonsense!
Thank you very much.
----
Yuuki Komata komata_at_complex.eng.hokudai.ac.jp
Received on Fri Sep 20 2002 - 01:03:48 PDT
