AMBER Archive (2002)

Subject: Re: Defining Restraints in Sander

From: John Bushnell (bushnell_at_chem.ucsb.edu)
Date: Thu Jul 18 2002 - 19:44:16 CDT

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
>