remarks dgtest3.inp remarks test metric matrix distrance geometry module -- remarks basic tests on four connected atoms remarks John Kuszewski and Axel T. Brunger remarks ================================== topology reset @CNS_TOPPAR:protein-allhdg.top end {* this is the DG-version of this file *} segment name="TRYP" chain LINK PEPP HEAD - * TAIL + PRO END { LINK to PRO } LINK PEPT HEAD - * TAIL + * END FIRSt PROP TAIL + PRO END { nter for PRO } FIRSt NTER TAIL + * END LAST CTER HEAD - * END sequence trp end end end parameter @CNS_TOPPAR:protein-allhdg.param nbonds repel = 0.8 end end coor ATOM 1 CA TRP 1 1.331 1.246 0.096 1.00 0.00 TRYP ATOM 2 HA TRP 1 1.571 0.780 1.039 1.00 0.00 TRYP ATOM 3 CB TRP 1 2.535 2.085 -0.418 1.00 0.00 TRYP ATOM 4 HB1 TRP 1 2.239 2.586 -1.319 1.00 0.00 TRYP ATOM 5 HB2 TRP 1 2.751 2.850 0.315 1.00 0.00 TRYP ATOM 6 CG TRP 1 3.804 1.229 -0.669 1.00 0.00 TRYP ATOM 7 CD1 TRP 1 4.717 0.866 0.299 1.00 0.00 TRYP ATOM 8 HD1 TRP 1 4.659 1.099 1.355 1.00 0.00 TRYP ATOM 9 CD2 TRP 1 4.351 0.653 -1.938 1.00 0.00 TRYP ATOM 10 NE1 TRP 1 5.724 0.123 -0.275 1.00 0.00 TRYP ATOM 11 HE1 TRP 1 6.486 -0.256 0.211 1.00 0.00 TRYP ATOM 12 CE2 TRP 1 5.557 -0.035 -1.629 1.00 0.00 TRYP ATOM 13 CE3 TRP 1 3.937 0.642 -3.303 1.00 0.00 TRYP ATOM 14 HE3 TRP 1 3.030 1.139 -3.603 1.00 0.00 TRYP ATOM 15 CZ2 TRP 1 6.307 -0.689 -2.607 1.00 0.00 TRYP ATOM 16 HZ2 TRP 1 7.219 -1.201 -2.337 1.00 0.00 TRYP ATOM 17 CZ3 TRP 1 4.699 -0.019 -4.279 1.00 0.00 TRYP ATOM 18 HZ3 TRP 1 4.371 -0.014 -5.308 1.00 0.00 TRYP ATOM 19 CH2 TRP 1 5.879 -0.680 -3.932 1.00 0.00 TRYP ATOM 20 HH2 TRP 1 6.459 -1.186 -4.691 1.00 0.00 TRYP ATOM 21 C TRP 1 0.137 2.181 0.303 1.00 0.00 TRYP ATOM 22 OT1 TRP 1 -0.629 2.346 -0.631 1.00 0.00 TRYP ATOM 23 OT2 TRP 1 0.010 2.715 1.393 1.00 0.00 TRYP ATOM 24 N TRP 1 0.945 0.198 -0.894 1.00 0.00 TRYP ATOM 25 HT1 TRP 1 1.555 -0.635 -0.775 1.00 0.00 TRYP ATOM 26 HT2 TRP 1 -0.048 -0.074 -0.740 1.00 0.00 TRYP ATOM 27 HT3 TRP 1 1.057 0.571 -1.858 1.00 0.00 TRYP END flags include noe cdihe end {* delete everything except one dihedral angle *} delete selection=( not ( name ca or name cb or name cg or name cd1 ) ) end {* =============================================================== *} {* test 1: test dihedral angle restraints *} {* =============================================================== *} restraints dihedral nassign=10 assign ( name ca ) ( name cb ) ( name cg ) ( name cd1 ) 1. 70. 0.01 2 end flags include cdih end set seed=12345 end mmdg verbose off iacc=0.01 tacc=0.01 bacc=0.001 pacc=0.01 random metrize (all) 100 end pick dihedral ( name ca ) ( name cb ) ( name cg ) ( name cd1 ) geometry print angles print bonds {* =============================================================== *} {* test 2: test inconsistency handling *} {* =============================================================== *} restraints dihedral nassign=10 assign ( name ca ) ( name cb ) ( name cg ) ( name cd1 ) 1. 70. 0.01 2 assign ( name ca ) ( name cb ) ( name cg ) ( name cd1 ) 1. 80. 0.01 2 end set seed=12345 end mmdg verbose off iacc=0.01 tacc=0.01 bacc=0.001 pacc=0.01 random metrize (all) 100 end pick dihedral ( name ca ) ( name cb ) ( name cg ) ( name cd1 ) geometry {* =============================================================== *} {* test 3: test flags (turning on/off of terms) *} {* =============================================================== *} flags exclude cdihe end set seed=12345 end mmdg verbose off iacc=0.01 tacc=0.01 bacc=0.001 pacc=0.01 random metrize (all) 100 end pick dihedral ( name ca ) ( name cb ) ( name cg ) ( name cd1 ) geometry print angles print bonds {* =============================================================== *} {* test 4: test coordinate reference *} {* =============================================================== *} structure reset end segment name="TRYP" chain LINK PEPP HEAD - * TAIL + PRO END { LINK to PRO } LINK PEPT HEAD - * TAIL + * END FIRSt PROP TAIL + PRO END { nter for PRO } FIRSt NTER TAIL + * END LAST CTER HEAD - * END sequence trp end end end coor ATOM 1 CA TRP 1 1.331 1.246 0.096 1.00 0.00 TRYP ATOM 2 HA TRP 1 1.571 0.780 1.039 1.00 0.00 TRYP ATOM 3 CB TRP 1 2.535 2.085 -0.418 1.00 0.00 TRYP ATOM 4 HB1 TRP 1 2.239 2.586 -1.319 1.00 0.00 TRYP ATOM 5 HB2 TRP 1 2.751 2.850 0.315 1.00 0.00 TRYP ATOM 6 CG TRP 1 3.804 1.229 -0.669 1.00 0.00 TRYP ATOM 7 CD1 TRP 1 4.717 0.866 0.299 1.00 0.00 TRYP ATOM 8 HD1 TRP 1 4.659 1.099 1.355 1.00 0.00 TRYP ATOM 9 CD2 TRP 1 4.351 0.653 -1.938 1.00 0.00 TRYP ATOM 10 NE1 TRP 1 5.724 0.123 -0.275 1.00 0.00 TRYP ATOM 11 HE1 TRP 1 6.486 -0.256 0.211 1.00 0.00 TRYP ATOM 12 CE2 TRP 1 5.557 -0.035 -1.629 1.00 0.00 TRYP ATOM 13 CE3 TRP 1 3.937 0.642 -3.303 1.00 0.00 TRYP ATOM 14 HE3 TRP 1 3.030 1.139 -3.603 1.00 0.00 TRYP ATOM 15 CZ2 TRP 1 6.307 -0.689 -2.607 1.00 0.00 TRYP ATOM 16 HZ2 TRP 1 7.219 -1.201 -2.337 1.00 0.00 TRYP ATOM 17 CZ3 TRP 1 4.699 -0.019 -4.279 1.00 0.00 TRYP ATOM 18 HZ3 TRP 1 4.371 -0.014 -5.308 1.00 0.00 TRYP ATOM 19 CH2 TRP 1 5.879 -0.680 -3.932 1.00 0.00 TRYP ATOM 20 HH2 TRP 1 6.459 -1.186 -4.691 1.00 0.00 TRYP ATOM 21 C TRP 1 0.137 2.181 0.303 1.00 0.00 TRYP ATOM 22 OT1 TRP 1 -0.629 2.346 -0.631 1.00 0.00 TRYP ATOM 23 OT2 TRP 1 0.010 2.715 1.393 1.00 0.00 TRYP ATOM 24 N TRP 1 0.945 0.198 -0.894 1.00 0.00 TRYP ATOM 25 HT1 TRP 1 1.555 -0.635 -0.775 1.00 0.00 TRYP ATOM 26 HT2 TRP 1 -0.048 -0.074 -0.740 1.00 0.00 TRYP ATOM 27 HT3 TRP 1 1.057 0.571 -1.858 1.00 0.00 TRYP END flags exclude * include bond dihe angl impr vdw end {* delete everything except Ca and substituents *} delete selection=( not ( name ca or name cb or name c or name n or name ha ) ) end do (x=x+4.) ( name ha ) coor copy end mmdg reference=parameters verbose off iacc=0.01 tacc=0.01 bacc=0.001 pacc=0.01 random metrize (all) 100 end set mess=off end coor fit end set mess=on end coor rms end do (z=-z) ( all ) set mess=off end coor fit end set mess=on end coor rms end coor swap end coor copy end do (refx=x ) ( all ) do (refy=y) ( all ) do (refz=z) ( all ) mmdg reference=coordinates verbose off iacc=0.01 tacc=0.01 bacc=0.001 pacc=0.01 random metrize (all) 100 end set mess=off end coor fit end set mess=on end coor rms end do (z=-z) ( all ) set mess=off end coor fit end set mess=on end coor rms end if ( $RESULT > 0.1 ) then do (z=-z) ( all ) end if print angles print impropers print dihedrals stop