NMR Restraints Grid

Result table
 (Save to zip file containing files for each block)

image	mrblock_id	pdb_id	cing	stage	position	program	type	subtype
	12458	1szy	cing	1-original	15	XPLOR/CNS	protocol	structure calculation

! make-template.inp -- Build extended structure for local geometry reference
! Dave Schweisguth , 27 Apr 1996
! Derived from nmr/generate_template.inp

set seed=@xplor.seed end  ! Use xplor -s

set echo=off message=off end  ! Normal use
!set echo=on message=all end  ! Auxiliary file debugging

structure @rsf.inp end
parameter @XPLORLIB:toppar/dna-rna-allatom.par end

set echo=on message=all end

vector ident (x) (all)   ! Set X coordinate to atom number(!)
vector do (x=x/10) (all)
vector do (y=random(0.5)) (all)
vector do (z=random(0.5)) (all)
vector do (fbeta=50) (all)  ! Friction coefficient, in 1/ps
vector do (mass=100) (all)  ! Heavy masses, in amu

parameter
    nbonds
 cutnb=5.5
 rconst=20
 nbxmod=-2
 repel=0.9 ! Repulsive non-bonded energy only
 wmin=0.1
 tolerance=1
 rexp=2  ! default
 irexp=2  ! default
 inhibit=0.25
    end       
end 

! Parameter set may or may not contain dihedral energies

flags exclude * include bond angle dihe vdw end
minimize powell nstep=200 nprint=10 end

flags include impr end
minimize powell nstep=200 nprint=10 end

dynamics verlet
    nstep=200
    timestep=0.001 ! default
    iasvel=maxwell
    firsttemp=300
    tcoupling=true
    tbath=300
    nprint=50
    iprfrq=0  
end

parameter 
    nbonds
 rconst=2
 nbxmod=-3
 repel=0.75 ! Repulsive non-bonded energy only
    end
end

minimize powell nstep=400 nprint=25 end 

dynamics verlet
    nstep=1000
    timestep=0.005
    iasvel=maxwell
    firsttemp=300
    tcoupling=true 
    tbath=300
    nprint=100
    iprfrq=0
end

! H-building won't actually place protons, since we're using a fully protonated
!   topology/parameter set, but it may improve their positions
! We're using "nbonds repel", so the "elec" flag is irrelevant

flags exclude vdw end
vector do (mass=1) (name h*) 
hbuild selection=(name h*) phistep=360 end

flags include vdw end
minimize powell nstep=800 nprint=50 end

! Analyze and write out the final structure.
! Total energy should be no more than about 100. If it is, it is probably
! because one or more purines are trapped in a crumpled conformation.

flags exclude * include bond angle dihe impr vdw end

print threshold=0.05 bonds          
evaluate ($rms_bond=$result)
evaluate ($v_bond=$violations)
print threshold=5 angles
evaluate ($rms_angl=$result)
evaluate ($v_angl=$violations)
print threshold=15 dihedrals
evaluate ($rms_dihe=$result)
evaluate ($v_dihe=$violations)
print threshold=5 impropers
evaluate ($rms_impr=$result)
evaluate ($v_impr=$violations)

set echo=off message=off end

display Energy:      bond $bond, angle $angl, dihedral $dihe,
display              improper $impr, VdW $vdw, total $ener
display RMSD:        bond $rms_bond, angle $rms_angl, dihedral $rms_dihe,
display              improper $rms_impr
display Violations:  bond $v_bond, angle $v_angl, dihedral $v_dihe,
display              improper $v_impr

set echo=on message=all end

write coordinates output=template.pdb end  

stop

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