NMR Restraints Grid |
Result table
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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