* file mmfptest3.inp * test of MMFP primary hydration shell with betha-turn and 50 waters * stream datadir.def read RTF card unit 5 * TOPOLOGY FILE FOR PROTEINS USING EXPLICIT HYDROGEN ATOMS: VERSION 19 * RESIDUES ADDED: FOR formyl group in gramicidin A (with new atom type CFOR) * EAM ethanolamine tail (-NH-CH2-CH2-OH) is attached to the C terminus. * NMA N-methylacetamide * PALI, a 16 carbon aldehyde, is palmitolic acid minus the oh group * PCGL phosphocholine-glycerol polar head * WPOL H2O Water Stillinger polarization model * OPOL Oxygen Stillinger polarization model * HPOL hydrogen Stillinger polarization model * HPAT Path integral for Stillinger polarization model * 20 1 ! Version number MASS 1 H 1.00800 ! hydrogen which can h-bond to neutral atom MASS 2 HC 1.00800 ! - " - charged atom MASS 3 HA 1.00800 ! aliphatic hydrogen MASS 4 HT 1.00800 ! TIPS3P WATER HYDROGEN MASS 5 LP 0.0 ! ST2 LONE PAIR MASS 10 CT 12.01100 ! aliphatic carbon MASS 11 C 12.01100 ! carbonyl carbon MASS 12 CH1E 13.01900 ! extended atom carbon w/ one hydrogen MASS 13 CH2E 14.02700 ! - " - two MASS 14 CH3E 15.03500 ! - " - three MASS 15 CR1E 13.01900 ! - " - in aromatic ring w/ one H MASS 16 CM 12.01100 ! carbon in carbonmonoxide MASS 17 CFOR 13.01900 ! CH1E carbon for the formyl group of gramicidin A MASS 31 N 14.00670 ! peptide nitrogen with no hydrogens attached MASS 32 NR 14.00670 ! nitrogen in aromatic ring with no hydrogens MASS 33 NP 14.00670 ! pyrole nitrogen !MASS 34 NH1E 15.01470 ! extended atom peptide nitrogen with one hydrogen !MASS 35 NH2E 16.02270 ! - " - two -"- !MASS 36 NH3E 17.03070 ! - " - three -"- !MASS 37 NC2E 16.02270 ! extended atom charged guanidinium nitrogen w/ 2 H MASS 38 NH1 14.00670 ! peptide nitrogen bound to one hydrogen MASS 39 NH2 14.00670 ! - " - two -"- MASS 40 NH3 14.00670 ! nitrogen bound to three hydrogens MASS 41 NC2 14.00670 ! charged guanidinuim nitrogen bound to two hydrogens MASS 42 NT 14.00670 ! for choline head of DPPC MASS 51 O 15.99940 ! carbonyl oxygen MASS 52 OC 15.99940 ! carboxy oxygen !MASS 53 OH1E 17.00740 ! extended atom hydroxy oxygen !MASS 54 OH2E 18.01540 ! extended atom water MASS 53 OPOL 16.00000 ! Oxygen in polarization model PM1 MASS 54 HPOL 1.00000 ! Hydrogen in polarization model PM1 MASS 55 OH1 15.99940 ! hydroxy oxygen MASS 56 OH2 15.99940 ! ST2 water oxygen MASS 57 OM 15.99940 ! oxygen in carbonmonoxide MASS 58 OT 15.99940 ! TIPS3P WATER OXYGEN MASS 59 OS 15.99940 ! ester oxygen MASS 60 O2 15.99940 ! Phosphate group P=O !--------------------------------------------------------------------------- MASS 71 P 30.97400 ! phosphate group from RNA MASS 81 S 32.06000 ! sulphur MASS 82 SH1E 33.06800 ! extended atom sulphur with one hydrogen MASS 91 FE 55.84700 ! iron DECL -C DECL -O DECL +N DECL +H DECL +CA !MAKE THE OUT OF RESIDUE DECLARATIONS DECL -C1 DECL -C2 DECL -C3 DECL -C4 DECL +C1 DECL +C2 DECL +C3 DECL +C4 DECL -O2 DECL +O2 AUTOGENERATE ANGLES DEFA FIRS NTER LAST CTER RESI ALA 0.00000 GROU ATOM N NH1 -0.35 ATOM H H 0.25 ATOM CA CH1E 0.10 GROU ATOM CB CH3E 0.00 GROU ATOM C C 0.55 ATOM O O -0.55 BOND N CA CA C C +N C O N H BOND CA CB DIHE -C N CA C N CA C +N CA C +N +CA IMPH N -C CA H C CA +N O CA N C CB DONO H N ACCE O C IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 RESI NEND 0.00000 ! GROU ! \ ATOM N NH1 -0.35 ! N - CA ATOM H H 0.25 ! / ATOM CA CH3E 0.10 ! H BOND N CA N H IMPH N -C CA H RESI CFIR 0.00000 ! / GROU ! CA - C ATOM CA CH3E 0.00 ! \\ ATOM C C 0.55 ! O ATOM O O -0.55 BOND CA C C +N C O DIHE CA C +N +CA IMPH C CA +N O RESI TIP3 .000 ! TIPS3P WATER MODEL GROUP ATOM OH2 OT -0.834 ATOM H1 HT 0.417 ATOM H2 HT 0.417 BOND OH2 H1 OH2 H2 H1 H2 ! THE LAST BOND IS NEEDED FOR SHAKE ANGLE H1 OH2 H2 ACCE OH2 PATC FIRS NONE LAST NONE END open read card unit 1 name @0param19.prm read PARAM card unit 1 close unit 1 read sequence TIP3 50 generate BULK setup noangle nodihe read sequence card * BETT * 4 CFIR ALA ALA NEND generate BETT warning setup first none last none MMFP !constraint on center of mass of peptide at origin GEO sphere RCM force 5.0 select segid BETT show end !setup the reference peptide atoms BHEL select segid BETT .and. ( .not. type H* ) end !setup the solvent potential on water SHEL DRSH 3.81115 select type OH2 end END read coor card unit 5 * 50000 STEPS PRODUCTION DYNAMICS OF BETT IN 50 WATERS * WITH DRSH EQUAL 3.81115 * DATE: 7/ 2/94 8:52:15 CREATED BY USER: * 168 1 1 TIP3 OH2 -4.91736 -1.73136 2.05049 BULK 1 0.00000 2 1 TIP3 H1 -4.77835 -1.18414 2.82344 BULK 1 0.00000 3 1 TIP3 H2 -4.98894 -1.10976 1.32611 BULK 1 0.00000 4 2 TIP3 OH2 5.84540 -3.59129 2.88944 BULK 2 0.00000 5 2 TIP3 H1 6.66272 -3.21106 2.56750 BULK 2 0.00000 6 2 TIP3 H2 5.33058 -3.75742 2.09976 BULK 2 0.00000 7 3 TIP3 OH2 6.51328 -0.95102 -0.68313 BULK 3 0.00000 8 3 TIP3 H1 5.73053 -0.48959 -0.98416 BULK 3 0.00000 9 3 TIP3 H2 6.63048 -1.66148 -1.31380 BULK 3 0.00000 10 4 TIP3 OH2 1.14879 1.15433 -6.02066 BULK 4 0.00000 11 4 TIP3 H1 0.70134 1.14649 -5.17452 BULK 4 0.00000 12 4 TIP3 H2 2.04213 1.43138 -5.81716 BULK 4 0.00000 13 5 TIP3 OH2 0.55519 5.11489 -2.10521 BULK 5 0.00000 14 5 TIP3 H1 -0.15052 4.71834 -1.59438 BULK 5 0.00000 15 5 TIP3 H2 0.82998 5.87180 -1.58770 BULK 5 0.00000 16 6 TIP3 OH2 7.28347 1.60790 -0.29997 BULK 6 0.00000 17 6 TIP3 H1 6.43781 1.64716 -0.74668 BULK 6 0.00000 18 6 TIP3 H2 7.40632 0.67995 -0.09984 BULK 6 0.00000 19 7 TIP3 OH2 -0.59198 -3.97116 -5.90631 BULK 7 0.00000 20 7 TIP3 H1 -1.37564 -3.53514 -5.57166 BULK 7 0.00000 21 7 TIP3 H2 -0.88243 -4.40378 -6.70924 BULK 7 0.00000 22 8 TIP3 OH2 7.17928 5.53702 0.98266 BULK 8 0.00000 23 8 TIP3 H1 7.99549 5.99457 1.18435 BULK 8 0.00000 24 8 TIP3 H2 7.34142 5.11837 0.13728 BULK 8 0.00000 25 9 TIP3 OH2 2.51592 3.98700 -3.71116 BULK 9 0.00000 26 9 TIP3 H1 3.22023 4.33748 -3.16586 BULK 9 0.00000 27 9 TIP3 H2 1.71829 4.37554 -3.35192 BULK 9 0.00000 28 10 TIP3 OH2 3.67156 1.95138 6.97507 BULK 10 0.00000 29 10 TIP3 H1 3.30860 1.07932 6.82013 BULK 10 0.00000 30 10 TIP3 H2 3.66655 2.04767 7.92740 BULK 10 0.00000 31 11 TIP3 OH2 7.89673 -2.30168 1.62777 BULK 11 0.00000 32 11 TIP3 H1 7.41401 -1.91059 0.89957 BULK 11 0.00000 33 11 TIP3 H2 8.81023 -2.06784 1.46325 BULK 11 0.00000 34 12 TIP3 OH2 -3.17972 5.76338 2.12857 BULK 12 0.00000 35 12 TIP3 H1 -2.78087 6.42149 1.55932 BULK 12 0.00000 36 12 TIP3 H2 -2.43781 5.28661 2.50073 BULK 12 0.00000 37 13 TIP3 OH2 1.82252 -3.29944 -4.79609 BULK 13 0.00000 38 13 TIP3 H1 1.41308 -2.68247 -4.18950 BULK 13 0.00000 39 13 TIP3 H2 1.08949 -3.69234 -5.26993 BULK 13 0.00000 40 14 TIP3 OH2 3.40299 1.81634 -4.89407 BULK 14 0.00000 41 14 TIP3 H1 4.35017 1.92562 -4.80958 BULK 14 0.00000 42 14 TIP3 H2 3.04047 2.66811 -4.65052 BULK 14 0.00000 43 15 TIP3 OH2 -0.53692 -1.05679 -5.90553 BULK 15 0.00000 44 15 TIP3 H1 0.05943 -0.35712 -6.17212 BULK 15 0.00000 45 15 TIP3 H2 0.02795 -1.70813 -5.48971 BULK 15 0.00000 46 16 TIP3 OH2 -2.15594 6.99392 -0.33106 BULK 16 0.00000 47 16 TIP3 H1 -2.36346 7.77914 -0.83761 BULK 16 0.00000 48 16 TIP3 H2 -1.43093 6.58698 -0.80540 BULK 16 0.00000 49 17 TIP3 OH2 -4.31664 2.16920 -0.03165 BULK 17 0.00000 50 17 TIP3 H1 -4.72341 2.49857 0.76978 BULK 17 0.00000 51 17 TIP3 H2 -3.60609 1.60540 0.27407 BULK 17 0.00000 52 18 TIP3 OH2 -3.13368 -3.43682 -4.63249 BULK 18 0.00000 53 18 TIP3 H1 -3.38669 -2.65177 -5.11819 BULK 18 0.00000 54 18 TIP3 H2 -3.86252 -3.59274 -4.03189 BULK 18 0.00000 55 19 TIP3 OH2 -5.31929 1.93317 -2.83872 BULK 19 0.00000 56 19 TIP3 H1 -5.13890 2.77934 -3.24822 BULK 19 0.00000 57 19 TIP3 H2 -5.05689 2.04778 -1.92535 BULK 19 0.00000 58 20 TIP3 OH2 -1.78404 -3.94964 -2.14511 BULK 20 0.00000 59 20 TIP3 H1 -2.67767 -4.28114 -2.05700 BULK 20 0.00000 60 20 TIP3 H2 -1.54019 -4.15398 -3.04789 BULK 20 0.00000 61 21 TIP3 OH2 -3.54659 -4.31322 0.03822 BULK 21 0.00000 62 21 TIP3 H1 -2.67408 -4.67379 0.19612 BULK 21 0.00000 63 21 TIP3 H2 -3.88324 -4.10872 0.91062 BULK 21 0.00000 64 22 TIP3 OH2 3.02937 -3.94510 -2.16640 BULK 22 0.00000 65 22 TIP3 H1 2.63393 -4.06311 -3.03008 BULK 22 0.00000 66 22 TIP3 H2 2.28660 -3.80145 -1.57998 BULK 22 0.00000 67 23 TIP3 OH2 4.44280 -1.97738 -4.95631 BULK 23 0.00000 68 23 TIP3 H1 4.76151 -1.65407 -5.79900 BULK 23 0.00000 69 23 TIP3 H2 3.66392 -2.48915 -5.17463 BULK 23 0.00000 70 24 TIP3 OH2 5.00167 1.45240 -1.89405 BULK 24 0.00000 71 24 TIP3 H1 4.45647 0.73812 -2.22388 BULK 24 0.00000 72 24 TIP3 H2 4.53222 2.24805 -2.14464 BULK 24 0.00000 73 25 TIP3 OH2 3.93295 6.20224 0.23936 BULK 25 0.00000 74 25 TIP3 H1 4.09366 5.47881 0.84522 BULK 25 0.00000 75 25 TIP3 H2 4.44669 6.92898 0.59171 BULK 25 0.00000 76 26 TIP3 OH2 0.54916 -1.74933 -3.00198 BULK 26 0.00000 77 26 TIP3 H1 0.53156 -2.17193 -2.14330 BULK 26 0.00000 78 26 TIP3 H2 0.03401 -0.95080 -2.88705 BULK 26 0.00000 79 27 TIP3 OH2 4.75261 -4.59555 0.44334 BULK 27 0.00000 80 27 TIP3 H1 4.39084 -4.47862 -0.43511 BULK 27 0.00000 81 27 TIP3 H2 5.17915 -5.45200 0.41518 BULK 27 0.00000 82 28 TIP3 OH2 7.62886 4.28381 -1.32973 BULK 28 0.00000 83 28 TIP3 H1 8.10583 4.18969 -2.15427 BULK 28 0.00000 84 28 TIP3 H2 7.84784 3.49457 -0.83437 BULK 28 0.00000 85 29 TIP3 OH2 -0.98274 -2.43978 0.83343 BULK 29 0.00000 86 29 TIP3 H1 -1.82402 -2.29795 0.39941 BULK 29 0.00000 87 29 TIP3 H2 -0.36189 -1.91126 0.33200 BULK 29 0.00000 88 30 TIP3 OH2 -4.72203 -3.55646 -2.33183 BULK 30 0.00000 89 30 TIP3 H1 -4.39640 -3.85339 -1.48210 BULK 30 0.00000 90 30 TIP3 H2 -5.57197 -3.16102 -2.13827 BULK 30 0.00000 91 31 TIP3 OH2 -2.17340 0.59655 0.46401 BULK 31 0.00000 92 31 TIP3 H1 -1.61539 0.44529 1.22688 BULK 31 0.00000 93 31 TIP3 H2 -1.98724 -0.13930 -0.11918 BULK 31 0.00000 94 32 TIP3 OH2 1.95377 3.48231 2.46362 BULK 32 0.00000 95 32 TIP3 H1 2.07148 3.77662 3.36682 BULK 32 0.00000 96 32 TIP3 H2 2.83394 3.50258 2.08797 BULK 32 0.00000 97 33 TIP3 OH2 4.64312 4.68016 -1.85107 BULK 33 0.00000 98 33 TIP3 H1 5.53389 4.48403 -1.56074 BULK 33 0.00000 99 33 TIP3 H2 4.36079 5.40151 -1.28878 BULK 33 0.00000 100 34 TIP3 OH2 -5.15630 3.89840 1.95546 BULK 34 0.00000 101 34 TIP3 H1 -5.89792 4.45322 1.71378 BULK 34 0.00000 102 34 TIP3 H2 -4.40458 4.49096 1.95952 BULK 34 0.00000 103 35 TIP3 OH2 3.25925 -0.55713 -2.47375 BULK 35 0.00000 104 35 TIP3 H1 3.46524 -1.05038 -3.26779 BULK 35 0.00000 105 35 TIP3 H2 2.46479 -0.96938 -2.13446 BULK 35 0.00000 106 36 TIP3 OH2 -5.71826 -0.72577 -3.50924 BULK 36 0.00000 107 36 TIP3 H1 -5.62531 0.16014 -3.15888 BULK 36 0.00000 108 36 TIP3 H2 -5.12463 -0.75055 -4.25972 BULK 36 0.00000 109 37 TIP3 OH2 -5.40401 -0.31934 -0.36275 BULK 37 0.00000 110 37 TIP3 H1 -5.34054 -0.76584 -1.20705 BULK 37 0.00000 111 37 TIP3 H2 -5.06422 0.55974 -0.53003 BULK 37 0.00000 112 38 TIP3 OH2 5.57167 -2.72531 -2.48270 BULK 38 0.00000 113 38 TIP3 H1 5.37412 -2.07294 -3.15473 BULK 38 0.00000 114 38 TIP3 H2 4.73840 -3.17014 -2.32774 BULK 38 0.00000 115 39 TIP3 OH2 4.70221 4.57232 2.44190 BULK 39 0.00000 116 39 TIP3 H1 5.60087 4.29357 2.26600 BULK 39 0.00000 117 39 TIP3 H2 4.55592 4.34528 3.36021 BULK 39 0.00000 118 40 TIP3 OH2 4.36071 -2.73462 4.82284 BULK 40 0.00000 119 40 TIP3 H1 5.04708 -2.76667 5.48925 BULK 40 0.00000 120 40 TIP3 H2 4.77876 -3.07357 4.03127 BULK 40 0.00000 121 41 TIP3 OH2 -1.07679 3.68753 2.50617 BULK 41 0.00000 122 41 TIP3 H1 -0.12735 3.59663 2.42534 BULK 41 0.00000 123 41 TIP3 H2 -1.36885 2.84811 2.86157 BULK 41 0.00000 124 42 TIP3 OH2 1.74150 -3.14703 4.57838 BULK 42 0.00000 125 42 TIP3 H1 2.64164 -2.85212 4.44051 BULK 42 0.00000 126 42 TIP3 H2 1.82918 -4.04768 4.89041 BULK 42 0.00000 127 43 TIP3 OH2 -2.84107 -1.12696 -1.93866 BULK 43 0.00000 128 43 TIP3 H1 -3.51830 -0.87145 -2.56500 BULK 43 0.00000 129 43 TIP3 H2 -2.53061 -1.97578 -2.25385 BULK 43 0.00000 130 44 TIP3 OH2 -1.51256 4.14542 -0.38914 BULK 44 0.00000 131 44 TIP3 H1 -2.14706 4.85887 -0.32108 BULK 44 0.00000 132 44 TIP3 H2 -1.78643 3.51622 0.27819 BULK 44 0.00000 133 45 TIP3 OH2 1.35553 7.22998 -0.40203 BULK 45 0.00000 134 45 TIP3 H1 0.98570 7.90213 0.17040 BULK 45 0.00000 135 45 TIP3 H2 2.22663 7.06157 -0.04278 BULK 45 0.00000 136 46 TIP3 OH2 4.46671 3.88331 5.21497 BULK 46 0.00000 137 46 TIP3 H1 4.35640 3.12743 5.79178 BULK 46 0.00000 138 46 TIP3 H2 4.69748 4.60237 5.80313 BULK 46 0.00000 139 47 TIP3 OH2 -4.76436 -4.53730 2.71015 BULK 47 0.00000 140 47 TIP3 H1 -5.19932 -3.71841 2.47252 BULK 47 0.00000 141 47 TIP3 H2 -5.46162 -5.08233 3.07485 BULK 47 0.00000 142 48 TIP3 OH2 2.96106 -0.66645 6.35113 BULK 48 0.00000 143 48 TIP3 H1 3.47752 -1.13050 5.69222 BULK 48 0.00000 144 48 TIP3 H2 2.16773 -1.19306 6.44882 BULK 48 0.00000 145 49 TIP3 OH2 0.58592 -3.95232 -0.63246 BULK 49 0.00000 146 49 TIP3 H1 0.25365 -3.62022 0.20153 BULK 49 0.00000 147 49 TIP3 H2 -0.19563 -4.07004 -1.17241 BULK 49 0.00000 148 50 TIP3 OH2 -3.57099 -0.61222 -5.31048 BULK 50 0.00000 149 50 TIP3 H1 -2.63102 -0.60497 -5.49114 BULK 50 0.00000 150 50 TIP3 H2 -3.91280 0.14427 -5.78705 BULK 50 0.00000 151 51 CFIR CA -1.75637 2.31802 -3.04372 BETT 1 0.00000 152 51 CFIR C -0.38912 1.76702 -2.73692 BETT 1 0.00000 153 51 CFIR O 0.21567 0.95462 -3.50845 BETT 1 0.00000 154 52 ALA N 0.15114 2.13092 -1.54200 BETT 2 0.00000 155 52 ALA H -0.41848 2.66833 -0.95283 BETT 2 0.00000 156 52 ALA CA 1.41597 1.68243 -1.05717 BETT 2 0.00000 157 52 ALA CB 2.09396 2.93833 -0.37395 BETT 2 0.00000 158 52 ALA C 1.06263 0.57276 -0.10307 BETT 2 0.00000 159 52 ALA O 0.64301 -0.50308 -0.48014 BETT 2 0.00000 160 53 ALA N 1.25737 0.83987 1.20838 BETT 3 0.00000 161 53 ALA H 1.31103 1.75018 1.56735 BETT 3 0.00000 162 53 ALA CA 1.21348 -0.21648 2.15944 BETT 3 0.00000 163 53 ALA CB 2.22946 0.02340 3.22045 BETT 3 0.00000 164 53 ALA C -0.06111 -0.17627 2.93576 BETT 3 0.00000 165 53 ALA O -0.78756 0.79136 2.93132 BETT 3 0.00000 166 54 NEND N -0.44138 -1.19488 3.71751 BETT 4 0.00000 167 54 NEND H 0.10243 -2.00009 3.84522 BETT 4 0.00000 168 54 NEND CA -1.73808 -1.30924 4.44015 BETT 4 0.00000 NBOND ctonnb 50.0 ctofnb 50.0 cutnb 14.0 wmin 1.2 - elec switch group cdie eps 1.0 - extend grad quadr - vdw vswitch vgroup !--------------------------------------------------------------------------- energy !dynamics shake tolerance 1.0e-06 bonh param scalar fbeta set 25.0 select .not. type H* end open write unfor unit 52 name @9primsh.trj title * 500 steps production of the betha-turn in 50 vaters * starting from primsh_0.crd * DYNAMICS strt nstep 1000 timestp 0.001 iprfrq 1000 - nprint 100 - - iasvel 1 firstt 300.0 finalt 300.0 tstruc 300.0 - langevin tbath 300.0 rbuf 0.0 - - inbfrq 5 ihbfrq 0 ilbfrq 0 - - iunread -1 - iunwrite -1 - iuncrd 52 nsavcrd 5 - iunvelo -1 nsavvelo 0 - kunit -1 open write card unit 1 name @9primsh_1.crd write coor card unit 1 * after one psec * steps production dynamics of BETT in 50 waters * with drsh equal ?DRSH * stop