remark param1.inp remark ======== remark remark test for atom-based parameter lookup remark Thomas Simonson, June 91. topology residue test atom a type=a charge=0.0 mass=1.0 end atom b type=b charge=0.0 mass=1.0 end atom c type=c charge=0.0 mass=1.0 end atom d type=d charge=0.0 mass=1.0 end atom e type=e charge=0.0 mass=1.0 end atom f type=f charge=0.0 mass=1.0 end atom g type=g charge=0.0 mass=1.0 end atom h type=h charge=0.0 mass=1.0 end atom i type=i charge=0.0 mass=1.0 end atom j type=j charge=0.0 mass=1.0 end atom k type=k charge=0.0 mass=1.0 end atom l type=l charge=0.0 mass=1.0 end atom m type=m charge=0.0 mass=1.0 end atom n type=n charge=0.0 mass=1.0 end bond a b bond c d !permutation angle c b a !permutation angle a b d dihedral d c b a !permutation dihedral a b c e ! dihedral a b c e ! {* double *} dihedral a f g b {* WILDCARD-match *} improper d c b a !permutation improper a b c e ! improper a b c e ! {* DOUBLE *} improper f a b g ! {* WILDCARD-match *} improper a h i j ! improper a b k l ! improper a m n b ! acceptor b none acceptor c g donor e a donor i d end end !topology segment name=test molecule number=1 name=test end end coor ATOM 1 A TEST 1 0.000 0.000 2.000 1.00 0.00 TEST ATOM 2 B TEST 1 1.000 0.000 1.000 1.00 0.00 TEST ATOM 3 C TEST 1 -1.000 1.000 0.000 1.00 0.00 TEST ATOM 4 D TEST 1 2.000 1.000 0.000 1.00 0.00 TEST ATOM 5 E TEST 1 0.000 1.000 0.000 1.00 0.00 TEST ATOM 6 F TEST 1 1.000 1.000 0.000 1.00 0.00 TEST ATOM 7 G TEST 1 0.000 -1.000 0.000 1.00 0.00 TEST ATOM 8 H TEST 1 1.000 -1.000 0.000 1.00 0.00 TEST ATOM 9 I TEST 1 -1.000 -1.000 0.000 1.00 0.00 TEST ATOM 10 J TEST 1 2.000 2.000 0.000 1.00 0.00 TEST ATOM 11 K TEST 1 3.000 3.000 0.000 1.00 0.00 TEST ATOM 12 L TEST 1 4.000 2.000 0.000 1.00 0.00 TEST ATOM 13 M TEST 1 5.000 1.000 0.000 1.00 0.00 TEST ATOM 14 N TEST 1 6.000 1.000 0.000 1.00 0.00 TEST END {* test error messages for missing parameters *} set abort=off end energy end parameter BOND A B 100.0 1.0 BOND (name D) (name C) 200.0 2.0 ANGLE (name A) (name B) (name C) 50.0 100.0 ANGLE A B D 60.0 120.0 DIHEDRAL (name A) (name B) (name C) (name D) 80.0 3 0.0 DIHEDRAL (name A) (name B) (name C) (name E) multiple 2 70.0 1 0.0 ! 40.0 0 0.0 ! {* double *} DIHEDRAL (all) (name F) (name G) (all) 30.0 4 180.0 IMPROPER A B C D 80.0 0 120.0 IMPROPER (name A) (name B) (name C) (name E) multiple 2 70.0 0 120.0 ! 40.0 0 120.0 ! {* double *} IMPROPER F X X G 30.0 2 -90.0 ! {* wildcards *} IMPROPER X H I J 10.0 0 180.0 ! IMPROPER (all) (all) (name K) (name L) 20.0 3 180.0 ! IMPROPER X M N X 30.0 0 180.0 ! NONBONDED A 0.1 1.0 0.1 1.0 NONBONDED B 0.1 1.0 0.1 1.0 NONBONDED (name B) 0.1 1.0 0.1 1.0 NONBONDED C 0.1 1.0 0.1 1.0 NONBONDED D 0.1 1.0 0.1 1.0 NONBONDED E 0.1 1.0 0.1 1.0 NONBONDED F 0.1 1.0 0.1 1.0 NONBONDED G 0.1 1.0 0.1 1.0 NONBONDED H 0.1 1.0 0.1 1.0 NONBONDED I 0.1 1.0 0.1 1.0 NONBONDED J 0.1 1.0 0.1 1.0 NONBONDED K 0.1 1.0 0.1 1.0 NONBONDED L 0.1 1.0 0.1 1.0 NONBONDED M 0.1 1.0 0.1 1.0 NONBONDED N 0.1 1.0 0.1 1.0 ? verbose end !parameter parameter nbonds end end energy end pick bond (name c) (name d) energy pick impr (name a) (name h) (name i) (name j) energy delete sele=(name b or name e) end pick bond (name c) (name d) energy pick impr (name a) (name h) (name i) (name j) energy !================================================= remarks second test structure delete sele=(all) end parameters reset end topology @CNS_TOPPAR:protein.top end parameter @CNS_TOPPAR:protein.param end parameter nbonds atom cdie shift eps=1.0 cutnb=100.0 nbxmod=5 vswitch end end segment name=tryp chain @CNS_TOPPAR:protein.link sequence TRP end end end coor ATOM 1 HT1 TRP 1 0.101 0.574 -1.385 1.00 0.00 TRYP ATOM 2 HT2 TRP 1 1.711 0.436 -1.904 1.00 0.00 TRYP ATOM 3 N TRP 1 1.067 0.302 -1.101 1.00 0.00 TRYP ATOM 4 HT3 TRP 1 1.080 -0.689 -0.791 1.00 0.00 TRYP ATOM 5 CA TRP 1 1.472 1.192 0.027 1.00 0.00 TRYP ATOM 6 CB TRP 1 2.696 2.026 -0.348 1.00 0.00 TRYP ATOM 7 CG TRP 1 3.922 1.169 -0.679 1.00 0.00 TRYP ATOM 8 CD2 TRP 1 4.295 0.679 -1.890 1.00 0.00 TRYP ATOM 9 CE2 TRP 1 5.424 -0.010 -1.601 1.00 0.00 TRYP ATOM 10 CE3 TRP 1 3.769 0.774 -3.155 1.00 0.00 TRYP ATOM 11 CD1 TRP 1 4.813 0.775 0.290 1.00 0.00 TRYP ATOM 12 NE1 TRP 1 5.727 0.046 -0.320 1.00 0.00 TRYP ATOM 13 HE1 TRP 1 6.094 -0.743 0.127 1.00 0.00 TRYP ATOM 14 CZ2 TRP 1 6.138 -0.677 -2.563 1.00 0.00 TRYP ATOM 15 CZ3 TRP 1 4.472 0.108 -4.148 1.00 0.00 TRYP ATOM 16 CH2 TRP 1 5.636 -0.605 -3.856 1.00 0.00 TRYP ATOM 17 C TRP 1 0.280 2.113 0.309 1.00 0.00 TRYP ATOM 18 O TRP 1 -0.402 2.481 -0.636 1.00 0.00 TRYP ATOM 19 OXT TRP 1 -0.106 2.192 1.459 1.00 0.00 TRYP END energy end parameter BOND (chem C) (chem C) 450.0 1.38 BOND (chem C) (chem CH1E) 405.0 1.52 ANGLE (chem C) (chem C) (chem C) 70.0 106.5 ANGLE (chem C) (chem C) (chem CH2E) 65.0 126.5 ANGLE (chem C) (chem CH1E) (chem CH1E) 70.0 110.0 DIHEdral (all) (chem C) (chem CH1E) (all) 0.0 3 0.0 IMPRoper (chem C) (all) (all) (chem C) 25.0 0 0.0 NONBONDED (chem C) 0.1200 3.7418 0.1 3.3854 NONBONDED (chem CH2E) 0.1142 3.9823 0.1 3.3854 !!!!! NONBONDED (chem CH1E) 0.0486 4.2140 0.1 3.3854 end print bonds print angles print dihedrals print impropers pick bond (chem C) (chem CH1E ) geom pick bond (chem C) (chem CH2E ) geom pick angle (chem C) (chem CH1E ) (chem CH1E ) geom pick angle (chem C) (chem CH1E ) (chem CH2E ) geom parameter ? end energy end parameter BOND (chem C) (chem CH2E) 405.0 1.52 ANGLE (chem C) (chem CH1E) (chem CH2E) 70.0 109.5 DIHEdral (all) (chem C) (chem CH2E) (all) 0.0 3 0.0 IMPRoper (chem C) (all) (all) (chem CH2E) 90.0 0 0.0 NONBONDED (chem CH2E) 0.1142 3.9823 0.1 3.3854 NONBonded (chem NH1) 0.2384 2.8509 0.2384 2.8509 NONBONDED (chem C) 0.1200 3.7418 0.1 3.3854 end print bonds print angles print dihedrals print impropers pick bond (chem C) (chem CH1E ) geom pick bond (chem C) (chem CH2E ) geom pick angle (chem C) (chem CH1E ) (chem CH1E ) geom pick angle (chem C) (chem CH1E ) (chem CH2E ) geom parameter ? end energy end parameter reset bonds ( all ) ( all ) 300. 1. angles ( all ) ( all ) ( all ) 300. 60. impropers ( all ) ( all ) ( all ) ( all ) 100. 1 0. dihedrals ( all ) ( all ) ( all ) ( all ) 100. 1 0. nonbonded ( chemical c* ) 0.1 4. 0.1 4. nonbonded ( not ( chemical c* ) ) 0.1 3. 0.1 3. end parameter ? verbose end energy end parameter bonds ( all ) ( all ) 600. 1. angles ( all ) ( all ) ( all ) 600. 60. impropers ( all ) ( all ) ( all ) ( all ) 200. 1 0. dihedrals ( all ) ( all ) ( all ) ( all ) 200. 1 0. nonbonded ( chemical c* ) 0.2 4. 0.2 4. nonbonded ( not ( chemical c* ) ) 0.2 3. 0.2 3. end parameter ? verbose end energy end parameter nonbonded ( chemical c ) 0.3 4. 0.3 4. nbfix ( chemical c ) ( not ( chemical c* ) ) 40. 50. 60. 70. end parameter ? verbose end energy end { test TOKEn features } flags exclude vdw pvdw end parameter BOND (chem C*) (chem C*) 50000.0 90. ANGLE (chem C*) (chem C*) (chem C*) 50000. 90. UB 50000. 90. DIHEdral (all) (chem C*) (chem C*) (all) 50000. 9 90. IMPRoper (chem C*) (all) (all) (chem C*) 50000. 9 90. verbose BOND (chem C*) (chem C*) TOKEN 10. ANGLE (chem C*) (chem C*) (chem C*) TOKEN 10. UB TOKEN TOKEN DIHEdral (all) (chem C*) (chem C*) (all) TOKEN 8 TOKEN IMPRoper (chem C*) (all) (all) (chem C*) TOKEN 7 TOKEN verbose BOND (chem C*) (chem C*) 40000. TOKEN ANGLE (chem C*) (chem C*) (chem C*) 40000. TOKEN UB TOKEN TOKEN DIHEdral (all) (chem C*) (chem C*) (all) 40000. TOKEN TOKEN IMPRoper (chem C*) (all) (all) (chem C*) 40000. TOKEN TOKEN verbose ANGLE (chem C*) (chem C*) (chem C*) TOKEN TOKEN UB 40000. TOKEN DIHEdral (all) (chem C*) (chem C*) (all) TOKEN TOKEN 10. IMPRoper (chem C*) (all) (all) (chem C*) TOKEN TOKEN 3. verbose ANGLE (chem C*) (chem C*) (chem C*) TOKEN TOKEN UB TOKEN 10. verbose end stop