[AMBER] How can I exert external force in the end of DNA?

From: mehdi bagherpoor <ms.nightsky.gmail.com>
Date: Thu, 19 Apr 2012 18:43:01 +0430

Dear Amber user

I am M.Bagherpour an M.Sc student of physics at Institute for Advanced
Studies in Basic Science (www.iasbs.ac.ir).

I am using Amber software for DNA simulation (Amber10). Specially in my
project I need to exert external force in the end of DNA, The DNA that I
want to simulate has 17 bp.

Also what is the meaning of r1 & r2 & r3 & r4 & rk2 & rk3 in:

       &rst iat=39,40,42,43, r1=0., r2=170., r3=170., r4=360., rk2 = 30.,
          rk3 = 30.,

I would appreciate your help.
Looking forward to hearing from you.

Best regards
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Received on Thu Apr 19 2012 - 07:30:03 PDT
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