AMBER Archive (2002)

Subject: Defining Restraints in Sander

From: Asif Rahaman (arahaman_at_chemdept.chem.ou.edu)
Date: Thu Jul 18 2002 - 15:21:59 CDT

     I am putting restraint on 2 atoms (2967 and 3295) in the protein at a
specific distance 6.0558 A with a force constant 950.0 and doing the
minimization. I define the restraint in the input file in the following way:
--------------------------------------------------------------------------
  &end
  &wt TYPE='END'
  &end
  &rst iat=2967,3295,0,0,
   iresid=0, irstyp=0, ifvari=0, imult=0, ir6=0, ifntyp=0,
   nstep1=0, nstep2=0,
   r1=6.0558, r2=9.1, r3=9.1, r4=9.5,
   rk2=950.0, rk3=950.0,
  &end
  &rst iat = 0,0,0,0,
  &end
----------------------------------------------
  After the minimization is completed when I view final structure, I found
that the atoms 2967 and 3295 are not at 6.0588 A away but they are around
10 A away.

  Could you please let me know if I am doing anything wrong in defining the
restraint in the input file. I have looked at the sander manual (amber 5 -
page 160-163 and page 174). It is confusing to me. Please help!!!!!!!!!!!!!!

With best regards, Asif