remark param1.inp remark ======== remark remark test for atom-based parameter lookup remark Thomas Simonson, June 91. rtf 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 !rtf segment name=test molecule number=1 name=test end end coor natoms=14 1 TEST A 0.0 0.0 2.0 TEST 1 0.0 2 TEST B 1.0 0.0 1.0 TEST 1 0.0 3 TEST C -1.0 1.0 0.0 TEST 1 0.0 4 TEST D 2.0 1.0 0.0 TEST 1 0.0 5 TEST E 0.0 1.0 0.0 TEST 1 0.0 6 TEST F 1.0 1.0 0.0 TEST 1 0.0 7 TEST G 0.0 -1.0 0.0 TEST 1 0.0 8 TEST H 1.0 -1.0 0.0 TEST 1 0.0 9 TEST I -1.0 -1.0 0.0 TEST 1 0.0 10 TEST J 2.0 2.0 0.0 TEST 1 0.0 11 TEST K 3.0 3.0 0.0 TEST 1 0.0 12 TEST L 4.0 2.0 0.0 TEST 1 0.0 13 TEST M 5.0 1.0 0.0 TEST 1 0.0 14 TEST N 6.0 1.0 0.0 TEST 1 0.0 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 AEXP 4 REXP 6 HAEX 4 AAEX 2 HBOND A B -3.00 3.0 HBOND D C -2.00 2.0 HBOND A C -3.00 3.0 HBOND D B -2.00 2.0 ? verbose end !parameter parameter nbonds end hbonds acceptor=true don=3.5 doff=4.0 dcut=4.5 aon=50.0 aoff=70. acut=91.0 tolerance=0.25 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 @TOPPAR:toph11.pro end parameter @TOPPAR:param11.pro end parameter nbonds atom cdie shift eps=1.0 cutnb=100.0 nbxmod=5 vswitch end end segment name=tryp chain @TOPPAR:toph11.pep sequence TRP end end end coor remarks TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, remarks AND CG 50 STEPS remarks EPS=R POTENTIAL natoms 19 1 TRP HT1 0.10124 0.57409 -1.38529 TRYP 1 0.00000 2 TRP HT2 1.71114 0.43637 -1.90440 TRYP 1 0.00000 3 TRP N 1.06717 0.30225 -1.10075 TRYP 1 0.00000 4 TRP HT3 1.07999 -0.68894 -0.79051 TRYP 1 0.00000 5 TRP CA 1.47212 1.19190 0.02727 TRYP 1 0.00000 6 TRP CB 2.69565 2.02615 -0.34753 TRYP 1 0.00000 7 TRP CG 3.92166 1.16873 -0.67893 TRYP 1 0.00000 8 TRP CD2 4.29511 0.67909 -1.89046 TRYP 1 0.00000 9 TRP CE2 5.42381 -0.01032 -1.60094 TRYP 1 0.00000 10 TRP CE3 3.76875 0.77367 -3.15481 TRYP 1 0.00000 11 TRP CD1 4.81252 0.77506 0.29018 TRYP 1 0.00000 12 TRP NE1 5.72693 0.04608 -0.32026 TRYP 1 0.00000 13 TRP HE1 6.09389 -0.74349 0.12669 TRYP 1 0.00000 14 TRP CZ2 6.13756 -0.67683 -2.56270 TRYP 1 0.00000 15 TRP CZ3 4.47167 0.10800 -4.14811 TRYP 1 0.00000 16 TRP CH2 5.63634 -0.60503 -3.85644 TRYP 1 0.00000 17 TRP C 0.27986 2.11295 0.30889 TRYP 1 0.00000 18 TRP OT1 -0.40216 2.48057 -0.63623 TRYP 1 0.00000 19 TRP OT2 -0.10570 2.19226 1.45887 TRYP 1 0.00000 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 AEXP 4 REXP 6 HAEX 4 AAEX 2 HBOND C CH1E -3.00 3.0 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