* generate model compound B, minimize and perform * vibrational analysis * !set identifier set id1 model_b set toppar $CHARMMDATA set top @toppar/top_all27_prot_lipid.rtf set par @toppar/par_all27_prot_lipid.prm set toppar top_mmtsb_example.str ! tolgrd setting: RMS force tolerance to exit minimizer set a 0.0001 ! read the topology open unit 9 read form name @top read rtf card unit 9 close unit 9 ! read the parameters open unit 9 read form name @par read para card unit 9 close unit 9 !stream toppar file with additional rtf/param information stream @toppar read sequence cards * cmpd model 1 * 1 mod1 generate a first none last none setup warn !generate preliminary IC table !ic generate !stop ic param ic seed 1 h11 1 c1 1 c2 ic build coor print !put molecule in geometry corresponding to global !minimum energy conformation and optimize prior !to frequency calculation coor init ic edit dihe 1 c1 1 c2 1 n3 1 n4 0.0 dihe 1 c2 1 n3 1 n4 1 c5 180.0 dihe 1 n3 1 n4 1 c5 1 c6 180.0 end ic seed 1 h11 1 c1 1 c2 ic build coor print !minimization with infinite cutoffs update cutnb 99.0 ctofnb 98.0 ctonnb 97.0 switch vswitch mini abnr nstep 200 nprint 10 mini nraph nstep 50 ic fill ic print !vibrational analysis MOLVIB NDI1 39 NDI2 39 NDI3 48 SECO !fix ndi3 GFX DIM 39 39 48 PRNT 0 IC 1 1 2 0 0 ! 1, C1-H11 1 1 3 0 0 ! 2, C1-H12 1 1 4 0 0 ! 3, C1-H13 1 1 5 0 0 ! 4, C1-C2 1 5 6 0 0 ! 5, C2-O2 1 5 7 0 0 ! 6, C2-N3 1 7 8 0 0 ! 7, N3-H3 1 7 9 0 0 ! 8, N3-N4 1 9 10 0 0 ! 9, N4-C5 1 10 11 0 0 ! 10, C5-H5 1 10 12 0 0 ! 11, C5-C6 1 12 13 0 0 ! 12, C6-H61 1 12 14 0 0 ! 13, C6-H62 1 12 15 0 0 ! 14, C6-H63 2 2 1 3 0 ! 15, H11-C1-H12 2 2 1 4 0 ! 16, H11-C1-H13 2 3 1 4 0 ! 17, H12-C1-H13 2 2 1 5 0 ! 18, H11-C1-C2 2 3 1 5 0 ! 19, H12-C1-C2 2 4 1 5 0 ! 20, H13-C1-C2 2 1 5 7 0 ! 21, C1-C2-N3 2 1 5 6 0 ! 22, C1-C2-O2 2 6 5 7 0 ! 23, O2-C2-N3 2 5 7 9 0 ! 24, C2-N3-N4 2 5 7 8 0 ! 25, C2-N3-H3 2 8 7 9 0 ! 26, H3-N3-N4 2 7 9 10 0 ! 27, N3-N4-C5 2 9 10 12 0 ! 28, N4-C5-C6 2 9 10 11 0 ! 29, N4-C5-H5 2 11 10 12 0 ! 30, H5-C5-N4 2 10 12 13 0 ! 31, C5-C6-H61 2 10 12 14 0 ! 32, C5-C6-H62 2 10 12 15 0 ! 33, C5-C6-H63 2 13 12 14 0 ! 34, H61-C6-H62 2 13 12 15 0 ! 35, H61-C6-H63 2 14 12 15 0 ! 36, H62-C6-H63 3 6 1 7 5 ! 37, O2-C1-N7-C2 wag 3 8 5 9 7 ! 38, H3-C2-N4-N3 wag 3 11 9 12 10 ! 39, H5-N4-C6-C5 wag 4 2 1 5 7 ! 40, H11-C1-C2-N3 4 3 1 5 7 ! 41, H12-C1-C2-N3 4 4 1 5 7 ! 42, H13-C1-C2-N3 4 1 5 7 9 ! 43, C1-C2-N3-N4 4 5 7 9 10 ! 44, C2-N3-N4-C5 4 7 9 10 12 ! 45, N3-N4-C5-C6 4 9 10 12 13 ! 46, N4-C5-C6-H61 4 9 10 12 14 ! 47, N4-C5-C6-H62 4 9 10 12 15 ! 48, N4-C5-C6-H63 UMAT 0 1 0 ! row normalization 1 1 1. 1 2 1. 1 3 1. 2 1 2. 2 2 -1. 2 3 -1. 3 2 1. 3 3 -1. 4 4 1. 5 5 1. 6 6 1. 7 7 1. 8 8 1. 9 9 1. 10 10 1. 11 11 1. 12 12 1. 12 13 1. 12 14 1. 13 12 2. 13 13 -1. 13 14 -1. 14 13 1. 14 14 -1. 15 15 1. 15 16 1. 15 17 1. 15 18 -1. 15 19 -1. 15 20 -1. 16 15 2. 16 16 -1. 16 17 -1. 17 16 1. 17 17 -1. 18 18 2. 18 19 -1. 18 20 -1. 19 19 1. 19 20 -1. 20 22 1. 20 23 -1. 21 21 2. 21 22 -1. 21 23 -1. 22 25 1. 22 26 -1. 23 24 2. 23 25 -1. 23 26 -1. 24 27 1. 25 29 1. 25 30 -1. 26 28 2. 26 29 -1. 26 29 -1. 27 34 1. 27 35 1. 27 36 1. 27 31 -1. 27 32 -1. 27 33 -1. 28 34 2. 28 35 -1. 28 36 -1. 29 35 1. 29 36 -1. 30 31 2. 30 32 -1. 30 33 -1. 31 32 2. 31 33 -1. 32 37 1. 33 38 1. 34 39 1. 35 40 1. 35 41 1. 35 42 1. 36 43 1. 37 44 1. 38 45 1. 39 46 1. 39 47 1. 39 48 1. -1 PED 8 15 2 1 12 2 2 13 2 3 14 2 15 27 2 16 28 2 17 29 2 18 30 2 19 31 1 sCH3 2 sCH3a 3 sCH3a' 4 sC1-C 5 sC=O 6 sC-N 7 sN-H 8 sN-N 9 sN=C 10 sC5-H 11 sC5-C 15 dCH3 16 dCH3a 17 dCH3a' 18 rCH3 19 rCH3' 20 rC=O 21 dC1CN 22 rNH 23 dC2NN 24 dN3NC 25 rC5H 26 dN4CC 32 wC=O 33 wNH 34 wC5H 35 tC1H3 36 tC2N 37 tN3N 38 tN4C 39 tC6H3 -1 END stop