This is an example input for MOLVIB analysis of guanine. this should be run using the nucleic acid topology file included with charmm. what MOLVIB does is determine the contributions of each mode to the individual vibrational frequencies in a fashion directly analogous to experimental analysis of vibration spectra. a helpful paper is Pulay et al., JACS, 101:2550 (1979) which describes the way to assign internal coordinates to different modes. if you're not sure of what i mean by modes, consider water. it has to hydrogen stretches, however, these are generally treated as symmetric and asymmetric stetching modes. the advantage of doing doing that is that it allows for direct comparison of experimental, ab initio and charmm vibrational spectra. my suggestion is that you first set up molvib to analyze the ab initio vibrational calculations (an example of this is below). you can then use the same MOLVIB setup to analyze the charmm vibrations IF you have the same atom order. an example of the input file for analysis of the ab initio vibrational results is after the charmm example. note that the ab initio analysis also uses the program charmm by inputing the gaussian cartesian coordinates and second derivative matix in cartesian cooridates. note that setting this up for the porphyrin will be difficult although the symmetry of the system will be helpful. also check the charmm documentation. alex !first generate and minimize the structure !prior to the vibrational analysis. ! guanine read sequence card * Guanine * 1 gua generate a first purg last none setup warn ic param ic seed 1 c4 1 n9 1 c8 ic build ic purge print ic update shift atom cutnb 99.0 energy mini nraph tolstp 0.00001 tolgrd 0.0 step 0.001 nstep 200 nprint 10 vibran diag end MOLVIB NDI1 42 NDI2 42 NDI3 61 SECO GFX PRNT 0 DIM 42 42 61 IC 1 11 12 0 0 !1 c6-o6 1 5 8 0 0 !2 c2-n2 1 6 7 0 0 !3 n1-h1 O6 1 15 16 0 0 !4 c8-h8 || 1 1 3 0 0 !5 n9-h9 C6 1 11 13 0 0 !6 c5-c6 / \ 1 13 2 0 0 !7 c4-c5 H1-N1 C5--N7\ 1 2 4 0 0 !8 n3-c4 | | C8-H8 1 4 5 0 0 !9 c2-n3 C2 C4--N9/ 1 5 6 0 0 !10 n1-c2 / \ / \ 1 6 11 0 0 !11 n1-c6 H21-N2 N3 H9 1 13 14 0 0 !12 c5-n7 | 1 14 15 0 0 !13 n7-c8 H22 1 15 1 0 0 !14 c8-n9 1 1 2 0 0 !15 c4-n9 2 6 11 13 0 !16 a1 6-mem ring 2 11 13 2 0 !17 a2 2 13 2 4 0 !18 a3 2 2 4 5 0 !19 a4 2 4 5 6 0 !20 a5 2 5 6 11 0 !21 a6 2 2 13 14 0 !22 a1 5-mem ring 2 13 14 15 0 !23 a2 2 14 15 1 0 !24 a3 2 15 1 2 0 !25 a4 2 1 2 13 0 !26 a5 2 12 11 13 0 !27 o6 bend 2 12 11 6 0 !28 2 8 5 6 0 !29 n2 bend 2 8 5 4 0 !30 2 7 6 11 0 !31 h1 bend 2 7 6 5 0 !32 2 16 15 1 0 !33 h8 bend 2 16 15 14 0 !34 2 3 1 2 0 !35 h9 bend 2 3 1 15 0 !36 3 12 6 13 11 !37 o6 wag 3 8 6 4 5 !38 n2 wag 3 7 5 11 6 !39 h1 wag 3 16 1 14 15 !40 h8 wag 3 3 2 15 1 !41 h9 wag 4 6 11 13 2 !42 t1 6-mem ring 4 11 13 2 4 !43 t2 4 13 2 4 5 !44 t3 4 2 4 5 6 !45 t4 4 4 5 6 11 !46 t5 4 5 6 11 13 !47 t6 4 1 2 13 14 !48 t1 5-mem ring 4 2 13 14 15 !49 t2 4 13 14 15 1 !50 t3 4 14 15 1 2 !51 t4 4 15 1 2 13 !52 t5 4 1 2 13 11 !53 bfly 4 4 2 13 14 !54 bfly 1 8 9 0 0 !55 n2-h21 1 8 10 0 0 !56 n2-h22 2 5 8 9 0 !57 c2-n2-h21 2 5 8 10 0 !58 c2-n2-h22 2 9 8 10 0 !59 h21-n2-h22 4 4 5 8 10 !60 n3-c2-n2-h22 4 6 5 8 9 !60 n1c2-n2-h21 UMAT 0 1 0 ! row normalization 1 1 1. 2 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. 13 13 1. 14 14 1. 15 15 1. 16 16 2. 16 17 -1. 16 18 -1. 16 19 2. 16 20 -1. 16 21 -1. 17 16 1. 17 17 -1. 17 18 1. 17 19 -1. 17 20 1. 17 21 -1. 18 17 1. 18 18 -1. 18 20 1. 18 21 -1. 19 22 -0.195440 19 23 0.511667 19 24 -0.632456 19 25 0.511667 19 26 -0.195440 20 22 -0.601501 20 23 0.371748 20 25 -0.371748 20 26 0.601501 21 27 1. 21 28 -1. 22 29 1. 22 30 -1. 23 31 1. 23 32 -1. 24 33 1. 24 34 -1. 25 35 1. 25 36 -1. 26 37 1. 27 38 1. 28 39 1. 29 40 1. 30 41 1. 31 42 1. 31 43 -1. 31 44 1. 31 45 -1. 31 46 1. 31 47 -1. 32 42 2. 32 43 -1. 32 44 -1. 32 45 2. 32 46 -1. 32 47 -1. 33 43 1. 33 44 -1. 33 46 1. 33 47 -1. 34 48 0.632456 34 49 -0.511667 34 50 0.195440 34 51 0.195440 34 52 -0.511667 35 49 0.371748 35 50 -0.601501 35 51 0.601501 35 52 -0.371748 36 53 1. 36 54 -1. 37 55 1. 37 56 -1. 38 55 1. 38 56 1. 39 57 1. 39 58 -1. 40 59 2. 40 57 -1. 40 58 -1. 41 60 1. 41 61 1. 42 61 1. 42 62 -1. -1 PED 0 15 1 sCO 2 sC2N 3 sN1H 4 sC8H 5 sN9H 6 sC5C6 7 sC4C5 8 sN3C4 9 sC2N3 10 sN1C2 11 sN1C6 12 sC5N7 13 sN7C8 14 sC8N9 15 sC4N9 16 dR6a 17 dR6t 18 dR6a' 19 dR5 20 dR5' 21 bCO 22 bC2N 23 bN1H 24 bC8H 25 bN9H 26 gCO 27 gC2N 28 gN1H 29 gC8H 30 gN9H 31 tR6 32 tR6a' 33 tR6a 34 tR5 35 tR5' 36 bfly 37 sNH2a 38 sNH2s 39 rockNH2 40 sciNH2 41 wNH2 42 tNH2 -1 END stop * charmm input for guanine g94 vibrational analysis * ! the second derivative matrix is read from an external ! file (fort.2) by charmm. in the gaussian output see ! "force constants in cartesian coordinates" ! NOTE: use IOP(7/33=1) in the gaussian input deck to get ! the force constants in cartesian coordinates in ! the gaussian output. if the vibrational calculation was ! performed without IOP(7/33=1) simply access the them from the ! checkpoint file with FREQ=(READFC) bomlev -1 MOLVIB NDI1 42 NDI2 42 NDI3 61 NATOm 16 NOTOpology GFX PRNT 0 DIM 42 42 61 CART 6 0 !Input orientation 1.722543 -1.480118 -0.003382 14.00700 0.533945 -0.835076 -0.000891 12.01100 1.850242 -2.466098 -0.011845 1.00800 -0.687231 -1.423678 0.003441 14.00700 -1.650556 -0.568552 -0.006269 12.01100 -1.468300 0.777738 -0.001377 14.00700 -2.258458 1.382341 -0.077005 1.00800 -2.941479 -1.001305 -0.060631 14.00700 -3.642470 -0.437952 0.367114 1.00800 -3.044455 -1.979733 0.096798 1.00800 -0.224569 1.454968 0.002453 12.01100 -0.211516 2.648251 -0.004453 15.99940 0.845679 0.497029 0.008130 12.01100 2.211945 0.675239 0.008679 14.00700 2.693911 -0.508432 0.002035 12.01100 3.734470 -0.759321 0.000716 1.00800 IC 1 11 12 0 0 !1 c6-o6 1 5 8 0 0 !2 c2-n2 1 6 7 0 0 !3 n1-h1 1 15 16 0 0 !4 c8-h8 1 1 3 0 0 !5 n9-h9 1 11 13 0 0 !6 c5-c6 1 13 2 0 0 !7 c4-c5 1 2 4 0 0 !8 n3-c4 1 4 5 0 0 !9 c2-n3 1 5 6 0 0 !10 n1-c2 1 6 11 0 0 !11 n1-c6 1 13 14 0 0 !12 c5-n7 1 14 15 0 0 !13 n7-c8 1 15 1 0 0 !14 c8-n9 1 1 2 0 0 !15 c4-n9 2 6 11 13 0 !16 a1 6-mem ring 2 11 13 2 0 !17 a2 2 13 2 4 0 !18 a3 2 2 4 5 0 !19 a4 2 4 5 6 0 !20 a5 2 5 6 11 0 !21 a6 2 2 13 14 0 !22 a1 5-mem ring 2 13 14 15 0 !23 a2 2 14 15 1 0 !24 a3 2 15 1 2 0 !25 a4 2 1 2 13 0 !26 a5 2 12 11 13 0 !27 o6 bend 2 12 11 6 0 !28 2 8 5 6 0 !29 n2 bend 2 8 5 4 0 !30 2 7 6 11 0 !31 h1 bend 2 7 6 5 0 !32 2 16 15 1 0 !33 h8 bend 2 16 15 14 0 !34 2 3 1 2 0 !35 h9 bend 2 3 1 15 0 !36 3 12 6 13 11 !37 o6 wag 3 8 6 4 5 !38 n2 wag 3 7 5 11 6 !39 h1 wag 3 16 1 14 15 !40 h8 wag 3 3 2 15 1 !41 h9 wag 4 6 11 13 2 !42 t1 6-mem ring 4 11 13 2 4 !43 t2 4 13 2 4 5 !44 t3 4 2 4 5 6 !45 t4 4 4 5 6 11 !46 t5 4 5 6 11 13 !47 t6 4 1 2 13 14 !48 t1 5-mem ring 4 2 13 14 15 !49 t2 4 13 14 15 1 !50 t3 4 14 15 1 2 !51 t4 4 15 1 2 13 !52 t5 4 1 2 13 11 !53 bfly 4 4 2 13 14 !54 bfly 1 8 9 0 0 !55 n2-h21 1 8 10 0 0 !56 n2-h22 2 5 8 9 0 !57 c2-n2-h21 2 5 8 10 0 !58 c2-n2-h22 2 9 8 10 0 !59 h21-n2-h22 4 4 5 8 10 !60 n3-c2-n2-h22 4 6 5 8 9 !60 n1c2-n2-h21 UMAT 0 1 0 ! row normalization 1 1 1. 2 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. 13 13 1. 14 14 1. 15 15 1. 16 16 2. 16 17 -1. 16 18 -1. 16 19 2. 16 20 -1. 16 21 -1. 17 16 1. 17 17 -1. 17 18 1. 17 19 -1. 17 20 1. 17 21 -1. 18 17 1. 18 18 -1. 18 20 1. 18 21 -1. 19 22 -0.195440 19 23 0.511667 19 24 -0.632456 19 25 0.511667 19 26 -0.195440 20 22 -0.601501 20 23 0.371748 20 25 -0.371748 20 26 0.601501 21 27 1. 21 28 -1. 22 29 1. 22 30 -1. 23 31 1. 23 32 -1. 24 33 1. 24 34 -1. 25 35 1. 25 36 -1. 26 37 1. 27 38 1. 28 39 1. 29 40 1. 30 41 1. 31 42 1. 31 43 -1. 31 44 1. 31 45 -1. 31 46 1. 31 47 -1. 32 42 2. 32 43 -1. 32 44 -1. 32 45 2. 32 46 -1. 32 47 -1. 33 43 1. 33 44 -1. 33 46 1. 33 47 -1. 34 48 0.632456 34 49 -0.511667 34 50 0.195440 34 51 0.195440 34 52 -0.511667 35 49 0.371748 35 50 -0.601501 35 51 0.601501 35 52 -0.371748 36 53 1. 36 54 -1. 37 55 1. 37 56 -1. 38 55 1. 38 56 1. 39 57 1. 39 58 -1. 40 59 2. 40 57 -1. 40 58 -1. 41 60 1. 41 61 1. 42 61 1. 42 62 -1. -1 FMAT 1 1 2 PED 0 15 1 sCO 2 sC2N 3 sN1H 4 sC8H 5 sN9H 6 sC5C6 7 sC4C5 8 sN3C4 9 sC2N3 10 sN1C2 11 sN1C6 12 sC5N7 13 sN7C8 14 sC8N9 15 sC4N9 16 dR6a 17 dR6t 18 dR6a' 19 dR5 20 dR5' 21 bCO 22 bC2N 23 bN1H 24 bC8H 25 bN9H 26 gCO 27 gC2N 28 gN1H 29 gC8H 30 gN9H 31 tR6 32 tR6a' 33 tR6a 34 tR5 35 tR5' 36 bfly 37 sNH2a 38 sNH2s 39 rockNH2 40 sciNH2 41 wNH2 42 tNH2 -1 SCALE 0.81 END stop