Questions and problems?

Docking with sander?

Hello, I'm trying to dock a molecule in an active site. Can anyone suggest an easy way to put a constraint on a residue in the active site and the small molecule being docked? Ideally, I would like to place a moderate force constant between the protein and the small molecule and run dynamics, then release the constraint and run production dynamics. The molecule is already very close to the correct position I would just like to give it a little push. I know I should be able to do this with SANDER but I can't figure out how to construct the input deck for a simple constraint between two molecules. 
Date: Wed, 30 Mar 94 11:01:42 PST
From: case@scripps.edu (David Case)
To: amber@cgl.ucsf.EDU
Subject: Re: Constraints between molecules
The restraints in Sander don't care about molecules if you use atom numbers, so try the following: 
  &rst  iat = , ,  r1=??. r2=??.....etc
This will make the constraint. You can use the NSTEP1,NSTEP2 variables to have it active for a while, and then be turned off. 
From: dap@portal.vpharm.com (David A. Pearlman)
Subject: Re: Constraints between molecules
Here's sample input which would do the following:
  1. Defines two centers of mass. COM1 is defined by:
    C1 in residue 1
    C1 in residue 2
    N2 in residue 3
    C1 in residue 4

    COM2 is defined by:
    C4 in residue 1
    O4 in residue 1
    N* in residue 1
    (These definitions are effected by the igr1/igr2 and grnam1/grnam2 variables; You can use up to 200 atoms to define a center-of-mass group)

  2. Set up a distance restraint between COM1 and COM2 which goes from a target value of 5.0A to 2.5A, with a force constant of 1.0, over steps 1-5000.
  3. Set up a distance restraint between COM1 and COM2 which remains fixed at the value of 2.5A as the force slowly constant decreases from 1.0 to 0.01 over steps 5001-10000.
  4. Sets up no distance restraint past step 10000, so that free (unrestrained) dynamics takes place past this step.
All the variables are defined/described in the manual. By reference to this sample input, you should be able to figure out what is being done... 
 &rst iat=-1,-1,1,1,
    atnam(1)='DUMM',atnam(2)='DUMM',
    nstep1=1,nstep2=5000,
    iresid=1,irstyp=0,ifvari=1,ninc=0,imult=0,ir6=0,ifntyp=0,
    r1=0.00000E+00,r2=5.0000,r3=5.0000,r4=99.000,rk2=1.0000,rk3=1.0000,
    r1a=0.00000E+00,r2a=2.5000,r3a=2.5000,r4a=99.000,rk2a=1.0000,rk3a=1.0000,
    igr1 = 2,3,4,5,0,
    grnam1(1)='C1',grnam1(2)='C1',grnam1(3)='N2',grnam1(4)='C1',
    igr2 = 1,1,1,0,
    grnam2(1)='C4',grnam2(2)='O4',grnam2(3)='N*',
 &end
 &rst iat=-1,-1,1,1,
    atnam(1)='DUMM',atnam(2)='DUMM',
    nstep1=5001,nstep2=10000,
    iresid=1,irstyp=0,ifvari=1,ninc=0,imult=0,ir6=0,ifntyp=0,
    r1=0.00000E+00,r2=2.5000,r3=2.5000,r4=99.000,rk2=1.0000,rk3=1.0000,
    r1a=0.00000E+00,r2a=2.5000,r3a=2.5000,r4a=99.000,rk2a=1.0000,rk3a=0.0100,
    igr1 = 2,3,4,5,0,
    grnam1(1)='C1',grnam1(2)='C1',grnam1(3)='N2',grnam1(4)='C1',
    igr2 = 1,1,1,0,
    grnam2(1)='C4',grnam2(2)='O4',grnam2(3)='N*',
 &end
 &rst iat=0,  &end