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

&rst iat =, , r1=??. r2=??.....etc

From: dap@portal.vpharm.com (David A. Pearlman) Subject: Re: Constraints between molecules

- 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) - 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.
- 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.
- Sets up no distance restraint past step 10000, so that free (unrestrained) dynamics takes place past this step.

&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