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
Received on Thu Jul 18 2002 - 13:21:59 PDT
