AMBER Archive (2000)

Subject: Re: Harmonic restraints on distances in sander

From: Marios Philippopoulos (mphilip_at_sickkids.on.ca)
Date: Wed Mar 08 2000 - 13:13:12 CST

Hi Vickie,

Just a clarification. Would the following restrained dynamics input file work?
Suppose I am imposing a single restraint between atoms 3 and 5:

 &cntrl
   imin=0, irest=1, ntx=7,.......,
   .........,
 &end
 &rst iat=3, 5, r1=..., r2=..., r3=..., r4=...,
      .........
 &end

I guess my question is whether I can put the restraint information right after
the dynamics information in an input file, as i did above. Also do the atom
numbers 3 and 5 correspond to the order of atoms in the topology file? From your
last message I gather they do.

Thanks,

Marios Philippopoulos

Vickie Tsui wrote:

> > Interesting, but in wich way is it possible to apply an harmonic
> > function to all bonds starting from a PDB file (without dg file) (I beg
> > aprdon if this is a trivial question)?
>
> Because the restraints input into AMBER are specified by the atom numbers
> (see section 4 of Sander), you can write a simple script that will go down
> the PDB file, take the atom numbers corresponding to the atom pairs for
> which you'd like distance restraints from the PDB file (that would give
> you the "IAT" variables). You can also calculate the distance between
> those atoms from the coordinates in the PDB file, and that would determine
> your "r2" and "r3" variables. Then the script can output those
> information (plus your desired r1, r4, and force constants) out in the
> format used for AMBER input restraints. You can do this for all atom
> pairs if you choose (that will give you a huge amount of restraints,
> depending on the size of your system), or for specified groups of the
> molecule.
>
> vickie
>
> The Scripps Research Institute
> 10550 North Torrey Pines Road, TPC-15
> La Jolla, CA 92037
>
> TEL: (858)784-9788
> FAX: (858)784-8896
>
> On Wed, 8 Mar 2000, Andrea Bernini wrote:
>
> > Vickie Tsui wrote:
> > >
> > > You could use distance restraints provided as part of the NMR refinement
> > > utilities to impose harmonic restraints on inter-atomic distances. Right
> > > now the penalty function is such that you can enter r1, r2, r3, r4 values.
> > > If R is the current distance, then the penalty function is:
> > >
> > > R < r1 linear
> > > r1 <= R < r2 parabolic
> > > r2 <= R < r3 Epenalty = 0
> > > r3 <= R < r4 parabolic
> > > r4 <= R linear
> > >
> > > If you want a purely harmonic function, set r1 to 0, r2=r3, and r4 to a
> > > large number, and that should work.
> > >
> > > vickie
> > 

--
Marios Philippopoulos, PhD
Structural Biology and Biochemistry Programme
Hospital for Sick Children
555 University Avenue
Toronto Ontario Canada M5G 1X8

mphilip_at_sickkids.on.ca