remarks dsele.inp remarks test double selection facilities remarks Thomas Simonson remarks ================ 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 pick bond (name CA) (name CB) energy pick angle (name CA) (name CB) (name CG) energy pick angle (name CA) (name CB) (name CG) geometry print threshold=3. angles {* subdivide molecule into two parts *} {=====================================} constraints interaction (name HT* or name N or name CA or name C or name OT*) (prev) weights bond 0.10 angle 0.20 dihe 0.30 impr 0.40 vdw 0.50 elec 0.60 end interaction (name HT* or name N or name CA or name C or name OT*) (prev) weights bond 0.90 angle 0.80 dihe 0.70 impr 0.60 vdw 0.50 elec 0.40 end interaction (name HT* or name N or name CA or name C or name OT*) (not (prev)) interaction (not (name HT* or name N or name CA or name C or name OT*)) (prev) ? end energy end pick bond (name CA) (name CB) energy pick angle (name CA) (name CB) (name CG) energy pick angle (name CA) (name CB) (name CG) geometry print threshold=3. angles vector show element (DX) (all) vector show element (DY) (all) vector show element (DZ) (all) {* Create a perturbation by placing an additional charge on HT1 *} {================================================================} constraints interaction (name HT1) (not name HT1) vweight * 0. elec 1. end interaction (not name HT1) (not name HT1) {zero vweight by default} end {* exp(-V/kT) averaging *} set seed=271828. end dynamics verlet iasvel=maxwell firsttemp=298. iasors=1 finaltemp=298. nstep=10 timestep=0.001 iprfrq=5 tcoupling=true tbath=298. trajectory=coor.dat nsavc=1 velocity=vel.dat nsavv=1 end display $AVE_PERT $AVE_ELEC {now calculate the free energy change "by hand" through the command language} constraints interaction (name HT1) (not name HT1) end energy accum=reset end flags exclude * include elec end {initializations for post-averaging of exp(-V/kT)} read trajectory begin=1 skip=1 stop=10 input=coor.dat end energy end evaluate ( $N=1) evaluate ( $V =-$ELEC/(298.*$KBOLTZ) ) evaluate ( $E = exp($V) ) {loop for post-averaging} while ($N < 10) loop main read trajectory next end energy end evaluate ( $V =-$ELEC/(298.*$KBOLTZ) ) evaluate ( $E = $E + exp($V) ) evaluate ( $N = $N+1.) end loop main evaluate ( $E = $E/$N) evaluate ( $A = LOG($E)) evaluate ( $A =-298.*$KBOLTZ*$A) display $A { free energy change } {* now test the hydrogen bonds term *} structure reset 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 coor remarks coordinates obtained from Greg Petsko remarks neutron diffraction structure of ribonuclease natoms=143 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 end ! ! ! TEST HBONDS ! parameter hbonds acceptor=true don=3.5 doff=4.0 dcut=5.0 aon=50.0 aoff=70. acut=90.0 end end print hbonds flags exclude * include hbonds end energy end cons interaction=( resid 1:2 ) ( prev) interaction=( resid 1:2 ) ( not prev) weights hbonds 0.5 end interaction=( resid 1:2 ) ( not prev) weights hbonds 0.5 end interaction=( not resid 1:2) (prev) end print hbonds end energy end constraints ? end stop