remarks +++++++++++++++HBUILDTES+++++++++++++++++++++++++++++++++++++ remarks Test run for the hydrogen position builder including waters remarks by Axel Brunger 1982/83 rtf @TOPPAR:toph11.pro @TOPPAR:toph11.wat end parameter @TOPPAR:param11.pro @TOPPAR:param11.wat end segment name=BET1 chain @TOPPAR:toph11.pep sequence PRO VAL ASN THR PHE VAL HIS end end end segment name=BET2 chain @TOPPAR:toph11.pep sequence SER ILE THR ASP CYS ARG GLU end end end segment name=TIP3 molecule name=TIP3 number=5 end end coor remarks coordinates obtained from Greg Petsko remarks neutron diffraction structure of ribonuclease natoms=158 1 1 PRO HT1 27.19210 7.94321 7.45578 BET1 1 0.00000 2 1 PRO HT2 26.44587 6.58714 6.75759 BET1 1 0.00000 3 1 PRO N 27.35563 7.06022 6.93119 BET1 1 0.00000 4 1 PRO CD 27.98205 7.40160 5.59861 BET1 1 0.00000 5 1 PRO CA 28.20449 6.19776 7.69905 BET1 1 0.00000 6 1 PRO CB 29.26930 5.66861 6.70704 BET1 1 0.00000 7 1 PRO CG 29.25018 6.59712 5.50731 BET1 1 0.00000 8 1 PRO C 28.79245 6.72230 8.99675 BET1 1 0.00000 9 1 PRO O 29.01698 5.99117 9.94926 BET1 1 0.00000 10 2 VAL N 29.05793 7.99757 8.89827 BET1 2 0.00000 11 2 VAL H 28.90648 8.59162 8.12529 BET1 2 0.00000 12 2 VAL CA 29.69531 8.70259 10.04107 BET1 2 0.00000 13 2 VAL CB 31.21849 8.59123 9.80615 BET1 2 0.00000 14 2 VAL CG1 31.95624 9.51129 10.73045 BET1 2 0.00000 15 2 VAL CG2 31.53416 7.15353 10.14212 BET1 2 0.00000 16 2 VAL C 29.24282 10.12954 10.12006 BET1 2 0.00000 17 2 VAL O 29.11877 10.74086 9.04753 BET1 2 0.00000 18 3 ASN N 28.99918 10.56153 11.33006 BET1 3 0.00000 19 3 ASN H 29.14509 10.00934 12.15126 BET1 3 0.00000 20 3 ASN CA 28.58851 11.94317 11.61679 BET1 3 0.00000 21 3 ASN CB 27.07362 12.09792 11.35263 BET1 3 0.00000 22 3 ASN CG 26.66547 13.54982 11.35519 BET1 3 0.00000 23 3 ASN OD1 27.22469 14.38041 10.63453 BET1 3 0.00000 24 3 ASN ND2 25.70533 13.96685 12.15177 BET1 3 0.00000 25 3 ASN HD21 25.23518 13.25760 12.74472 BET1 3 0.00000 26 3 ASN HD22 25.38801 14.94874 12.18306 BET1 3 0.00000 27 3 ASN C 28.96740 12.39629 13.05350 BET1 3 0.00000 28 3 ASN O 28.79346 11.60717 13.96907 BET1 3 0.00000 29 4 THR N 29.34952 13.66157 13.18942 BET1 4 0.00000 30 4 THR H 29.42904 14.26829 12.42567 BET1 4 0.00000 31 4 THR CA 29.65977 14.25600 14.48200 BET1 4 0.00000 32 4 THR CB 31.10227 14.80128 14.54509 BET1 4 0.00000 33 4 THR OG1 31.90032 13.79366 14.02498 BET1 4 0.00000 34 4 THR HG1 31.79428 12.85862 14.26452 BET1 4 0.00000 35 4 THR CG2 31.63905 15.22483 15.92743 BET1 4 0.00000 36 4 THR C 28.63678 15.40147 14.77181 BET1 4 0.00000 37 4 THR O 28.23957 16.22362 13.97472 BET1 4 0.00000 38 5 PHE N 28.26090 15.42758 16.05002 BET1 5 0.00000 39 5 PHE H 28.64239 14.75289 16.71221 BET1 5 0.00000 40 5 PHE CA 27.38060 16.42406 16.64194 BET1 5 0.00000 41 5 PHE CB 26.10794 15.92525 17.37850 BET1 5 0.00000 42 5 PHE CG 25.13360 15.39802 16.33829 BET1 5 0.00000 43 5 PHE CD1 24.29112 16.26010 15.67764 BET1 5 0.00000 44 5 PHE CD2 25.11930 13.99757 16.12183 BET1 5 0.00000 45 5 PHE CE1 23.39582 15.70752 14.75129 BET1 5 0.00000 46 5 PHE CE2 24.27159 13.45843 15.17240 BET1 5 0.00000 47 5 PHE CZ 23.38186 14.31091 14.47944 BET1 5 0.00000 48 5 PHE C 28.22539 17.23776 17.64523 BET1 5 0.00000 49 5 PHE O 29.07335 16.60378 18.34076 BET1 5 0.00000 50 6 VAL N 28.06751 18.56294 17.61240 BET1 6 0.00000 51 6 VAL H 27.34542 18.93657 17.02099 BET1 6 0.00000 52 6 VAL CA 28.78747 19.43654 18.56747 BET1 6 0.00000 53 6 VAL CB 29.61288 20.45107 17.74474 BET1 6 0.00000 54 6 VAL CG1 30.53574 21.31776 18.65057 BET1 6 0.00000 55 6 VAL CG2 30.35272 19.71917 16.65579 BET1 6 0.00000 56 6 VAL C 27.77446 20.03635 19.56409 BET1 6 0.00000 57 6 VAL O 26.77212 20.63117 19.10297 BET1 6 0.00000 58 7 HIS N 28.09145 19.92921 20.86590 BET1 7 0.00000 59 7 HIS H 28.92273 19.45190 21.12698 BET1 7 0.00000 60 7 HIS CA 27.26330 20.37964 21.96510 BET1 7 0.00000 61 7 HIS CB 27.32057 19.25145 23.03046 BET1 7 0.00000 62 7 HIS CG 26.89043 17.88403 22.61191 BET1 7 0.00000 63 7 HIS CD2 27.61824 16.74201 22.30620 BET1 7 0.00000 64 7 HIS ND1 25.58312 17.53996 22.60524 BET1 7 0.00000 65 7 HIS HD1 24.79289 18.19046 22.78528 BET1 7 0.00000 66 7 HIS CE1 25.50089 16.26163 22.22516 BET1 7 0.00000 67 7 HIS NE2 26.72091 15.75629 22.06307 BET1 7 0.00000 68 7 HIS HE2 26.92283 14.78054 21.78558 BET1 7 0.00000 69 7 HIS C 27.75132 21.65568 22.59755 BET1 7 0.00000 70 7 HIS OT1 28.76834 22.16748 22.13211 BET1 7 0.00000 71 7 HIS OT2 27.10252 22.10668 23.54018 BET1 7 0.00000 72 8 SER HT1 33.12422 19.90881 24.38770 BET2 1 0.00000 73 8 SER HT2 32.06885 20.28622 23.11216 BET2 1 0.00000 74 8 SER N 32.69556 19.55673 23.50799 BET2 1 0.00000 75 8 SER HT3 33.44528 19.33513 22.82212 BET2 1 0.00000 76 8 SER CA 31.91247 18.33600 23.79472 BET2 1 0.00000 77 8 SER CB 30.79948 18.66125 24.76826 BET2 1 0.00000 78 8 SER OG 30.05549 17.48966 24.74825 BET2 1 0.00000 79 8 SER HG 29.24969 17.53190 25.24887 BET2 1 0.00000 80 8 SER C 31.30875 17.86867 22.46213 BET2 1 0.00000 81 8 SER O 30.65674 18.70656 21.80456 BET2 1 0.00000 82 9 ILE N 31.65585 16.67174 21.98049 BET2 2 0.00000 83 9 ILE H 32.22105 16.04006 22.47290 BET2 2 0.00000 84 9 ILE CA 31.22831 16.16409 20.69920 BET2 2 0.00000 85 9 ILE CB 32.37001 16.24358 19.70104 BET2 2 0.00000 86 9 ILE CG2 32.99632 17.63213 19.45843 BET2 2 0.00000 87 9 ILE CG1 33.33544 15.23097 20.19653 BET2 2 0.00000 88 9 ILE CD 34.29426 14.75481 19.15477 BET2 2 0.00000 89 9 ILE C 30.76085 14.72678 20.90745 BET2 2 0.00000 90 9 ILE O 31.13488 14.02406 21.87124 BET2 2 0.00000 91 10 THR N 29.89373 14.31091 20.00726 BET2 3 0.00000 92 10 THR H 29.58767 14.85542 19.24095 BET2 3 0.00000 93 10 THR CA 29.30620 12.95040 19.97084 BET2 3 0.00000 94 10 THR CB 27.82835 12.79296 20.28527 BET2 3 0.00000 95 10 THR OG1 27.49452 13.40774 21.51424 BET2 3 0.00000 96 10 THR HG1 27.96319 13.18809 22.31903 BET2 3 0.00000 97 10 THR CG2 27.47324 11.32300 20.32527 BET2 3 0.00000 98 10 THR C 29.61784 12.46272 18.52028 BET2 3 0.00000 99 10 THR O 29.20474 13.10745 17.51340 BET2 3 0.00000 100 11 ASP N 30.31171 11.37677 18.45001 BET2 4 0.00000 101 11 ASP H 30.58467 10.84070 19.25531 BET2 4 0.00000 102 11 ASP CA 30.64776 10.71129 17.18770 BET2 4 0.00000 103 11 ASP CB 31.99652 10.06809 17.30670 BET2 4 0.00000 104 11 ASP CG 32.84881 10.52697 16.14697 BET2 4 0.00000 105 11 ASP OD1 33.47277 11.56185 16.26340 BET2 4 0.00000 106 11 ASP OD2 32.70667 9.62189 15.20831 BET2 4 0.00000 107 11 ASP C 29.67010 9.56505 16.98406 BET2 4 0.00000 108 11 ASP O 29.55062 8.85350 17.92682 BET2 4 0.00000 109 12 CYS N 29.10260 9.46445 15.84177 BET2 5 0.00000 110 12 CYS H 29.28555 10.14605 15.09854 BET2 5 0.00000 111 12 CYS CA 28.12815 8.48179 15.43759 BET2 5 0.00000 112 12 CYS CB 26.90109 9.22752 14.97287 BET2 5 0.00000 113 12 CYS SG 26.00696 10.23897 16.20134 BET2 5 0.00000 114 12 CYS C 28.70065 7.68307 14.27581 BET2 5 0.00000 115 12 CYS O 29.05154 8.28441 13.26739 BET2 5 0.00000 116 13 ARG N 28.84289 6.40512 14.51996 BET2 6 0.00000 117 13 ARG H 28.56754 6.00192 15.38988 BET2 6 0.00000 118 13 ARG CA 29.38734 5.47776 13.53668 BET2 6 0.00000 119 13 ARG CB 30.67100 4.94169 14.16347 BET2 6 0.00000 120 13 ARG CG 31.37675 4.04659 13.16378 BET2 6 0.00000 121 13 ARG CD 32.40045 5.02963 12.66419 BET2 6 0.00000 122 13 ARG NE 33.07164 5.45587 13.91111 BET2 6 0.00000 123 13 ARG HE 32.87922 4.99584 14.80361 BET2 6 0.00000 124 13 ARG CZ 33.95636 6.44467 13.93932 BET2 6 0.00000 125 13 ARG NH1 34.35910 7.15238 12.86731 BET2 6 0.00000 126 13 ARG HH11 33.96748 6.95347 11.95378 BET2 6 0.00000 127 13 ARG HH12 35.05100 7.89005 12.97194 BET2 6 0.00000 128 13 ARG NH2 34.55408 6.70003 15.12932 BET2 6 0.00000 129 13 ARG HH21 34.28357 6.22848 15.97154 BET2 6 0.00000 130 13 ARG HH22 35.22500 7.47494 15.17497 BET2 6 0.00000 131 13 ARG C 28.43803 4.29312 13.33099 BET2 6 0.00000 132 13 ARG O 27.89538 3.69523 14.23990 BET2 6 0.00000 133 14 GLU N 28.25630 4.03776 12.02046 BET2 7 0.00000 134 14 GLU H 28.65800 4.55501 11.25723 BET2 7 0.00000 135 14 GLU CA 27.32862 2.94566 11.64397 BET2 7 0.00000 136 14 GLU CB 27.29494 3.05894 10.09903 BET2 7 0.00000 137 14 GLU CG 25.98626 2.95910 9.41684 BET2 7 0.00000 138 14 GLU CD 25.96399 2.41229 7.98475 BET2 7 0.00000 139 14 GLU OE1 24.96674 1.89197 7.68109 BET2 7 0.00000 140 14 GLU OE2 27.05938 2.47641 7.38359 BET2 7 0.00000 141 14 GLU C 27.81263 1.62624 12.22358 BET2 7 0.00000 142 14 GLU OT1 28.84792 1.64328 12.88749 BET2 7 0.00000 143 14 GLU OT2 27.13898 0.62333 11.99275 BET2 7 0.00000 144 15 TIP3 OH2 30.95127 14.59622 10.76225 TIP3 1 0.00000 145 15 TIP3 H1 31.90628 14.64000 10.97871 TIP3 1 0.00000 146 15 TIP3 H2 31.03687 13.91616 10.04723 TIP3 1 0.00000 149 16 TIP3 OH2 28.53545 21.27360 26.28703 TIP3 2 0.00000 150 16 TIP3 H1 28.33687 21.52742 25.39300 TIP3 2 0.00000 151 16 TIP3 H2 28.24325 20.40768 26.48810 TIP3 2 0.00000 154 17 TIP3 OH2 12.85658 4.80269 14.21477 TIP3 3 0.00000 155 17 TIP3 H1 13.70097 4.34150 14.26914 TIP3 3 0.00000 156 17 TIP3 H2 12.70368 5.13254 15.10726 TIP3 3 0.00000 159 18 TIP3 OH2 33.41767 12.46310 11.57832 TIP3 4 0.00000 160 18 TIP3 H1 33.03679 11.69011 12.07688 TIP3 4 0.00000 161 18 TIP3 H2 34.34752 12.13363 11.63679 TIP3 4 0.00000 164 19 TIP3 OH2 32.69186 3.84422 16.96765 TIP3 5 0.00000 165 19 TIP3 H1 33.26508 3.07161 17.06511 TIP3 5 0.00000 166 19 TIP3 H2 32.10055 3.60806 16.25468 TIP3 5 0.00000 end coor copy end ! coor initial selection=( hydrogen ) end parameter hbonds acceptor=true don=4.7 doff=5.2 dcut=11.5 aon=50.0 aoff=70.0 acut=180.0 tolerance=3.0 !! tolerance for hbuild end nbonds atom cdie shift eps=1.0 cutnb=13.5 ctonnb=6.5 ctofnb=7.5 nbxmod=5 vswitch tolerance=3.0 !! increase tolerance for hbuild end end flags exclude * include dihe elec vdw hbon end hbuild selection=( hydrogen and not segid TIP3 ) print=true phistp=10.0 cutwat=5.7 end ! ! TEST HBUILD with waters ! hbuild selection=( segid TIP3 and hydrogen ) acceptors=( name O* ) !! acceptor definition print=true phistp=10.0 cutwat=5.7 end ! coor rms sele=( not ( hydrogen ) ) end ! write coor sele=( hydrogen ) end ! stop