Hi,
As another person noted, the force constant here is too
large. However, your constraint is at 9.1 Angstroms, not
6.0558 as you wanted. The constraining forces go up at
r < r2 and r > r3. The forces are parabolic between r1
and r2, and also between r3 and r4. They then become
linear at r < r1 and r > r4. So you should try something
like r2 = r3 = 6.0558.
- John
On Thu, 18 Jul 2002, Asif Rahaman wrote:
>
> 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 - 17:44:16 PDT
