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--- Regards Neeru Sharma On Mon, Dec 12, 2011 at 3:28 PM, FyD <fyd.q4md-forcefieldtools.org> wrote: > Dear Neeru, > > > Thanks Francois for your help. I was searching for the parameters since > > last week. I actually need these GDP parameters asap because I have to > > start my simulations on urgent basis. Rest all is already ready with me. > I > > would be thankful if you can now provide the GDP parameters, in whatever > > way suitable to you. For rest of the parameters, I can wait till the > > release of the database. > > Below, are two protonated forms for GDP & dGDP for the Duan et al. FF > in the .mol3 file format described at > http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php > > The FF atom types are these defined in Cornell et al. FF. The charges > were derived following the approach of Duan et al. (i.e. the RESP-A1B > charge model in R.E.D. Server). > > The key here is how the pyrophosphate is constructed, and how this > chemical group is handled. The prmtop/prmcrd file for GDP & dGDP > should be generated with the default leaprc file available for the > Duan et al. FF. On the top of that, you might decide to add your own > FF parameters. > > regards, > > > more dGDP*mol3.mol2 GDP*mol3.mol2 > > :::::::::::::: > dGDP1-mol3.mol2 > :::::::::::::: > .<TRIPOS>MOLECULE > dGDP1 > 40 42 3 0 1 > SMALL > USER_CHARGES > .<TRIPOS>ATOM > 1 OR 1.629083 1.717090 -1.624539 OS 1 P1M -0.3837 **** > 2 P 1.414045 1.561428 -0.000000 P 1 P1M 0.7819 **** > 3 OP1 0.238284 2.369306 0.390137 O2 1 P1M -0.6991 **** > 4 OP2 2.725620 1.690308 0.653481 O2 1 P1M -0.6991 **** > 5 OH 0.947166 0.000000 0.000000 OH 1 P1M -0.5586 **** > 6 HO 0.000000 0.000000 0.000000 HO 1 P1M 0.3832 **** > 7 OR 2.180160 2.783088 -3.864608 OS 2 P1 -0.3837 **** > 8 P 2.113142 3.117537 -2.254251 P 2 P1 0.7819 **** > 9 OP1 3.429966 3.455973 -1.672251 O2 2 P1 -0.6991 **** > 10 OP2 1.115705 4.144028 -1.914673 O2 2 P1 -0.6991 **** > 11 O3' 0.283734 3.439528 -7.053053 OH 3 G5 -0.6051 **** > 12 H3T -0.573627 3.042510 -7.112012 HO 3 G5 0.4297 **** > 13 C1' 3.157012 1.223238 -7.185655 CT 3 G5 0.1221 **** > 14 H1' 3.870905 1.146997 -7.991061 H2 3 G5 0.0947 **** > 15 C2' 1.751566 1.562677 -7.695078 CT 3 G5 -0.0509 **** > 16 H2'1 1.822622 2.119811 -8.623339 HC 3 G5 0.0547 **** > 17 H2'2 1.154083 0.677621 -7.869005 HC 3 G5 0.0547 **** > 18 C3' 1.216914 2.494962 -6.610783 CT 3 G5 0.0844 **** > 19 H3' 0.824324 1.930721 -5.773408 H1 3 G5 0.0828 **** > 20 C4' 2.491195 3.218614 -6.190880 CT 3 G5 0.1384 **** > 21 H4' 2.664458 4.033075 -6.889739 H1 3 G5 0.0884 **** > 22 C5' 2.499737 3.795058 -4.792988 CT 3 G5 0.0797 **** > 23 H5'1 3.486149 4.191768 -4.571586 H1 3 G5 0.0495 **** > 24 H5'2 1.765419 4.593479 -4.726436 H1 3 G5 0.0495 **** > 25 O4' 3.518964 2.258684 -6.324879 OS 3 G5 -0.3612 **** > 26 N2 3.748080 -3.181754 -9.894935 N2 3 G5 -0.7504 **** > 27 H21 3.904418 -2.439906 -10.541692 H 3 G5 0.3675 **** > 28 H22 4.287985 -3.999254 -10.075696 H 3 G5 0.3675 **** > 29 O6 3.540326 -4.499678 -5.536731 O 3 G5 -0.5626 **** > 30 C6 3.526223 -3.545097 -6.254098 C 3 G5 0.4183 **** > 31 C5 3.381078 -2.145936 -5.968124 CB 3 G5 0.2028 **** > 32 N7 3.222570 -1.482433 -4.773743 NB 3 G5 -0.6066 **** > 33 C8 3.135138 -0.245311 -5.095122 CK 3 G5 0.1268 **** > 34 H8 3.012835 0.573129 -4.419915 H5 3 G5 0.1446 **** > 35 N9 3.224774 -0.033524 -6.454205 N* 3 G5 0.0340 **** > 36 C4 3.383776 -1.258866 -7.008734 CB 3 G5 0.2074 **** > 37 N3 3.522159 -1.508299 -8.337985 NC 3 G5 -0.5840 **** > 38 C2 3.651897 -2.761944 -8.599194 CA 3 G5 0.5446 **** > 39 N1 3.661907 -3.734650 -7.652058 NA 3 G5 -0.3921 **** > 40 H1 3.696953 -4.692419 -7.929378 H 3 G5 0.3462 **** > .<TRIPOS>BOND > 1 5 6 1 > 2 2 3 1 > 3 2 4 1 > 4 2 5 1 > 5 1 2 1 > 6 1 8 1 > 7 8 9 1 > 8 8 10 1 > 9 7 8 1 > 10 7 22 1 > 11 39 40 1 > 12 38 39 1 > 13 37 38 1 > 14 36 37 1 > 15 35 36 1 > 16 33 34 1 > 17 33 35 1 > 18 32 33 1 > 19 31 32 1 > 20 31 36 1 > 21 30 31 1 > 22 30 39 1 > 23 29 30 1 > 24 26 27 1 > 25 26 28 1 > 26 26 38 1 > 27 22 23 1 > 28 22 24 1 > 29 20 21 1 > 30 20 22 1 > 31 20 25 1 > 32 18 19 1 > 33 18 20 1 > 34 15 16 1 > 35 15 17 1 > 36 15 18 1 > 37 13 14 1 > 38 13 15 1 > 39 13 25 1 > 40 13 35 1 > 41 11 12 1 > 42 11 18 1 > .<TRIPOS>SUBSTRUCTURE > 1 P1M 1 **** 0 **** **** > 2 P1 7 **** 0 **** **** > 3 G5 11 **** 0 **** **** > .<TRIPOS>HEADTAIL > 0 0 > 0 0 > .<TRIPOS>RESIDUECONNECT > 1 P OR 0 0 0 0 > 2 P OR 0 0 0 0 > 3 C5' C2' 0 0 0 0 > > :::::::::::::: > dGDP2-mol3.mol2 > :::::::::::::: > .<TRIPOS>MOLECULE > dGDP2 > 39 41 3 0 1 > SMALL > USER_CHARGES > .<TRIPOS>ATOM > 1 OR 1.893841 1.703592 -0.000000 OS 1 P2M -0.5717 **** > 2 P 1.511037 0.000000 0.000000 P 1 P2M 1.0294 **** > 3 OP1 2.142015 -0.481316 -1.285859 O2 1 P2M -0.8777 **** > 4 OP2 2.174586 -0.448283 1.273158 O2 1 P2M -0.8777 **** > 5 OP3 0.000000 0.000000 0.000000 O2 1 P2M -0.8777 **** > 6 OR 1.995803 4.123658 0.768655 OS 2 P1 -0.3837 **** > 7 P 1.410931 2.649617 1.209931 P 2 P1 0.7819 **** > 8 OP1 2.004585 2.136634 2.463610 O2 2 P1 -0.6991 **** > 9 OP2 -0.057956 2.602132 1.273137 O2 2 P1 -0.6991 **** > 10 O3' 0.820036 7.422734 -0.619580 OH 3 G5 -0.6051 **** > 11 H3T 0.491375 7.402947 -1.507137 HO 3 G5 0.4297 **** > 12 C1' 4.386681 6.925328 -0.153879 CT 3 G5 0.1221 **** > 13 H1' 5.100732 7.667758 0.167159 H2 3 G5 0.0947 **** > 14 C2' 3.257110 7.539157 -0.988918 CT 3 G5 -0.0509 **** > 15 H2'1 3.109521 8.574787 -0.701163 HC 3 G5 0.0547 **** > 16 H2'2 3.465631 7.502451 -2.049924 HC 3 G5 0.0547 **** > 17 C3' 2.036908 6.735330 -0.546570 CT 3 G5 0.0844 **** > 18 H3' 1.978516 5.794177 -1.079968 H1 3 G5 0.0828 **** > 19 C4' 2.370818 6.476316 0.918080 CT 3 G5 0.1384 **** > 20 H4' 2.077301 7.351318 1.492528 H1 3 G5 0.0884 **** > 21 C5' 1.716765 5.266305 1.546212 CT 3 G5 0.0797 **** > 22 H5'1 2.105924 5.125432 2.550262 H1 3 G5 0.0495 **** > 23 H5'2 0.641852 5.419589 1.593065 H1 3 G5 0.0495 **** > 24 O4' 3.776497 6.340570 0.955096 OS 3 G5 -0.3612 **** > 25 N2 8.311893 8.436001 -3.220489 N2 3 G5 -0.7504 **** > 26 H21 8.045466 9.242910 -2.699924 H 3 G5 0.3675 **** > 27 H22 9.283706 8.393528 -3.435554 H 3 G5 0.3675 **** > 28 O6 8.215471 3.893707 -3.584229 O 3 G5 -0.5626 **** > 29 C6 7.697596 4.826339 -3.047530 C 3 G5 0.4183 **** > 30 C5 6.591984 4.901683 -2.135147 CB 3 G5 0.2028 **** > 31 N7 5.799637 3.914673 -1.596719 NB 3 G5 -0.6066 **** > 32 C8 4.961952 4.536185 -0.852804 CK 3 G5 0.1268 **** > 33 H8 4.190623 4.089470 -0.264412 H5 3 G5 0.1446 **** > 34 N9 5.144542 5.902422 -0.859833 N* 3 G5 0.0340 **** > 35 C4 6.194143 6.130015 -1.684931 CB 3 G5 0.2074 **** > 36 N3 6.717874 7.351246 -1.972292 NC 3 G5 -0.5840 **** > 37 C2 7.709241 7.288563 -2.790798 CA 3 G5 0.5446 **** > 38 N1 8.192130 6.129073 -3.306283 NA 3 G5 -0.3921 **** > 39 H1 8.919029 6.158113 -3.989092 H 3 G5 0.3462 **** > .<TRIPOS>BOND > 1 2 3 1 > 2 2 4 1 > 3 2 5 1 > 4 1 2 1 > 5 1 7 1 > 6 7 8 1 > 7 7 9 1 > 8 6 7 1 > 9 6 21 1 > 10 38 39 1 > 11 37 38 1 > 12 36 37 1 > 13 35 36 1 > 14 34 35 1 > 15 32 33 1 > 16 32 34 1 > 17 31 32 1 > 18 30 31 1 > 19 30 35 1 > 20 29 30 1 > 21 29 38 1 > 22 28 29 1 > 23 25 26 1 > 24 25 27 1 > 25 25 37 1 > 26 21 22 1 > 27 21 23 1 > 28 19 20 1 > 29 19 21 1 > 30 19 24 1 > 31 17 18 1 > 32 17 19 1 > 33 14 15 1 > 34 14 16 1 > 35 14 17 1 > 36 12 13 1 > 37 12 14 1 > 38 12 24 1 > 39 12 34 1 > 40 10 11 1 > 41 10 17 1 > .<TRIPOS>SUBSTRUCTURE > 1 P2M 1 **** 0 **** **** > 2 P1 6 **** 0 **** **** > 3 G5 10 **** 0 **** **** > .<TRIPOS>HEADTAIL > 0 0 > 0 0 > .<TRIPOS>RESIDUECONNECT > 1 P OR 0 0 0 0 > 2 P OR 0 0 0 0 > 3 C5' C2' 0 0 0 0 > > :::::::::::::: > GDP1-mol3.mol2 > :::::::::::::: > .<TRIPOS>MOLECULE > GDP1 > 41 43 3 0 1 > SMALL > USER_CHARGES > .<TRIPOS>ATOM > 1 OR 1.629083 1.717090 -1.624539 OS 1 P1M -0.3837 **** > 2 P 1.414045 1.561428 -0.000000 P 1 P1M 0.7819 **** > 3 OP1 0.238284 2.369306 0.390137 O2 1 P1M -0.6991 **** > 4 OP2 2.725620 1.690308 0.653481 O2 1 P1M -0.6991 **** > 5 OH 0.947166 0.000000 0.000000 OH 1 P1M -0.5586 **** > 6 HO 0.000000 0.000000 0.000000 HO 1 P1M 0.3832 **** > 7 OR 2.180160 2.783088 -3.864608 OS 2 P1 -0.3837 **** > 8 P 2.113142 3.117537 -2.254251 P 2 P1 0.7819 **** > 9 OP1 3.429966 3.455973 -1.672251 O2 2 P1 -0.6991 **** > 10 OP2 1.115705 4.144028 -1.914673 O2 2 P1 -0.6991 **** > 11 O3' 0.235859 3.389144 -6.985710 OH 3 H5 -0.5979 **** > 12 H3T -0.549760 2.924347 -7.240119 HO 3 H5 0.4225 **** > 13 C1' 3.144479 1.223066 -7.185924 CT 3 H5 0.0958 **** > 14 H1' 3.854963 1.134377 -7.992250 H2 3 H5 0.1352 **** > 15 C2' 1.769457 1.611555 -7.738227 CT 3 H5 0.1426 **** > 16 H2' 1.164026 0.742954 -7.972509 H1 3 H5 0.0525 **** > 17 C3' 1.225285 2.477929 -6.600577 CT 3 H5 0.1180 **** > 18 H3' 0.882071 1.853051 -5.784415 H1 3 H5 0.0575 **** > 19 C4' 2.491199 3.218861 -6.190281 CT 3 H5 0.1484 **** > 20 H4' 2.667432 4.023447 -6.894457 H1 3 H5 0.0744 **** > 21 C5' 2.499737 3.795058 -4.792988 CT 3 H5 0.1070 **** > 22 H5'1 3.486239 4.191805 -4.571566 H1 3 H5 0.0417 **** > 23 H5'2 1.765376 4.593526 -4.726432 H1 3 H5 0.0417 **** > 24 O4' 3.512546 2.246881 -6.317354 OS 3 H5 -0.3628 **** > 25 O2' 2.018861 2.386430 -8.875757 OH 3 H5 -0.6069 **** > 26 H2T 1.200896 2.673520 -9.256746 HO 3 H5 0.4315 **** > 27 N2 3.283416 -3.212090 -9.903731 N2 3 H5 -0.7504 **** > 28 H21 3.451748 -2.480629 -10.559528 H 3 H5 0.3675 **** > 29 H22 3.761400 -4.061457 -10.110131 H 3 H5 0.3675 **** > 30 O6 3.226258 -4.509980 -5.533906 O 3 H5 -0.5626 **** > 31 C6 3.232560 -3.557859 -6.254459 C 3 H5 0.4183 **** > 32 C5 3.188824 -2.151682 -5.967660 CB 3 H5 0.2028 **** > 33 N7 3.137926 -1.477464 -4.769457 NB 3 H5 -0.6066 **** > 34 C8 3.111213 -0.238039 -5.090620 CK 3 H5 0.1268 **** > 35 H8 3.074165 0.587302 -4.414286 H5 3 H5 0.1446 **** > 36 N9 3.134990 -0.033906 -6.455059 N* 3 H5 0.0442 **** > 37 C4 3.189758 -1.268982 -7.011173 CB 3 H5 0.2074 **** > 38 N3 3.240653 -1.527755 -8.343828 NC 3 H5 -0.5840 **** > 39 C2 3.281257 -2.787269 -8.606479 CA 3 H5 0.5446 **** > 40 N1 3.282424 -3.757472 -7.656609 NA 3 H5 -0.3921 **** > 41 H1 3.247516 -4.716182 -7.930773 H 3 H5 0.3462 **** > .<TRIPOS>BOND > 1 5 6 1 > 2 2 3 1 > 3 2 4 1 > 4 2 5 1 > 5 1 2 1 > 6 1 8 1 > 7 8 9 1 > 8 8 10 1 > 9 7 8 1 > 10 7 21 1 > 11 40 41 1 > 12 39 40 1 > 13 38 39 1 > 14 37 38 1 > 15 36 37 1 > 16 34 35 1 > 17 34 36 1 > 18 33 34 1 > 19 32 33 1 > 20 32 37 1 > 21 31 32 1 > 22 31 40 1 > 23 30 31 1 > 24 27 28 1 > 25 27 29 1 > 26 27 39 1 > 27 25 26 1 > 28 21 22 1 > 29 21 23 1 > 30 19 20 1 > 31 19 21 1 > 32 19 24 1 > 33 17 18 1 > 34 17 19 1 > 35 15 16 1 > 36 15 17 1 > 37 15 25 1 > 38 13 14 1 > 39 13 15 1 > 40 13 24 1 > 41 13 36 1 > 42 11 12 1 > 43 11 17 1 > .<TRIPOS>SUBSTRUCTURE > 1 P1M 1 **** 0 **** **** > 2 P1 7 **** 0 **** **** > 3 H5 11 **** 0 **** **** > .<TRIPOS>HEADTAIL > 0 0 > 0 0 > .<TRIPOS>RESIDUECONNECT > 1 P OR 0 0 0 0 > 2 P OR 0 0 0 0 > 3 C5' C2' 0 0 0 0 > > :::::::::::::: > GDP2-mol3.mol2 > :::::::::::::: > .<TRIPOS>MOLECULE > GDP2 > 40 42 3 0 1 > SMALL > USER_CHARGES > .<TRIPOS>ATOM > 1 OR 1.893841 1.703592 -0.000000 OS 1 P2M -0.5717 **** > 2 P 1.511037 0.000000 0.000000 P 1 P2M 1.0294 **** > 3 OP1 2.142015 -0.481316 -1.285859 O2 1 P2M -0.8777 **** > 4 OP2 2.174586 -0.448283 1.273158 O2 1 P2M -0.8777 **** > 5 OP3 0.000000 0.000000 0.000000 O2 1 P2M -0.8777 **** > 6 OR 1.995803 4.123658 0.768655 OS 2 P1 -0.3837 **** > 7 P 1.410931 2.649617 1.209931 P 2 P1 0.7819 **** > 8 OP1 2.004585 2.136634 2.463610 O2 2 P1 -0.6991 **** > 9 OP2 -0.057956 2.602132 1.273137 O2 2 P1 -0.6991 **** > 10 O3' 0.807153 7.346216 -0.677414 OH 3 H5 -0.5979 **** > 11 H3T 0.613058 7.496931 -1.592602 HO 3 H5 0.4225 **** > 12 C1' 4.377949 6.925867 -0.162859 CT 3 H5 0.0958 **** > 13 H1' 5.098185 7.666175 0.147013 H2 3 H5 0.1352 **** > 14 C2' 3.245050 7.592646 -0.949365 CT 3 H5 0.1426 **** > 15 H2' 3.448435 7.618674 -2.014194 H1 3 H5 0.0525 **** > 16 C3' 2.052415 6.720992 -0.550847 CT 3 H5 0.1180 **** > 17 H3' 2.074237 5.784006 -1.094878 H1 3 H5 0.0575 **** > 18 C4' 2.370537 6.475797 0.918349 CT 3 H5 0.1484 **** > 19 H4' 2.086843 7.353411 1.487200 H1 3 H5 0.0744 **** > 20 C5' 1.716765 5.266305 1.546212 CT 3 H5 0.1070 **** > 21 H5'1 2.105960 5.125420 2.550354 H1 3 H5 0.0417 **** > 22 H5'2 0.641789 5.419597 1.593068 H1 3 H5 0.0417 **** > 23 O4' 3.778478 6.330509 0.943607 OS 3 H5 -0.3628 **** > 24 O2' 3.117080 8.880532 -0.418721 OH 3 H5 -0.6069 **** > 25 H2T 2.415361 9.341893 -0.856186 HO 3 H5 0.4315 **** > 26 N2 8.004150 8.448892 -3.569830 N2 3 H5 -0.7504 **** > 27 H21 7.755018 9.261659 -3.049460 H 3 H5 0.3675 **** > 28 H22 8.958517 8.424896 -3.854618 H 3 H5 0.3675 **** > 29 O6 7.998866 3.896472 -3.811886 O 3 H5 -0.5626 **** > 30 C6 7.497763 4.831050 -3.263042 C 3 H5 0.4183 **** > 31 C5 6.459256 4.904740 -2.274319 CB 3 H5 0.2028 **** > 32 N7 5.735335 3.913935 -1.652149 NB 3 H5 -0.6066 **** > 33 C8 4.939169 4.534251 -0.863883 CK 3 H5 0.1268 **** > 34 H8 4.223495 4.085975 -0.210549 H5 3 H5 0.1446 **** > 35 N9 5.081206 5.905459 -0.923405 N* 3 H5 0.0442 **** > 36 C4 6.063682 6.134839 -1.828833 CB 3 H5 0.2074 **** > 37 N3 6.532264 7.359285 -2.184760 NC 3 H5 -0.5840 **** > 38 C2 7.464585 7.298827 -3.070273 CA 3 H5 0.5446 **** > 39 N1 7.938971 6.137540 -3.589811 NA 3 H5 -0.3921 **** > 40 H1 8.616221 6.165086 -4.321987 H 3 H5 0.3462 **** > .<TRIPOS>BOND > 1 2 3 1 > 2 2 4 1 > 3 2 5 1 > 4 1 2 1 > 5 1 7 1 > 6 7 8 1 > 7 7 9 1 > 8 6 7 1 > 9 6 20 1 > 10 39 40 1 > 11 38 39 1 > 12 37 38 1 > 13 36 37 1 > 14 35 36 1 > 15 33 34 1 > 16 33 35 1 > 17 32 33 1 > 18 31 32 1 > 19 31 36 1 > 20 30 31 1 > 21 30 39 1 > 22 29 30 1 > 23 26 27 1 > 24 26 28 1 > 25 26 38 1 > 26 24 25 1 > 27 20 21 1 > 28 20 22 1 > 29 18 19 1 > 30 18 20 1 > 31 18 23 1 > 32 16 17 1 > 33 16 18 1 > 34 14 15 1 > 35 14 16 1 > 36 14 24 1 > 37 12 13 1 > 38 12 14 1 > 39 12 23 1 > 40 12 35 1 > 41 10 11 1 > 42 10 16 1 > .<TRIPOS>SUBSTRUCTURE > 1 P2M 1 **** 0 **** **** > 2 P1 6 **** 0 **** **** > 3 H5 10 **** 0 **** **** > .<TRIPOS>HEADTAIL > 0 0 > 0 0 > .<TRIPOS>RESIDUECONNECT > 1 P OR 0 0 0 0 > 2 P OR 0 0 0 0 > 3 C5' C2' 0 0 0 0 > > > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > -- Regards, Neeru Sharma Project Engineer, Molecular Modelling Team, Bioinformatics Group, Centre for Development of Advanced Computing (CDAC), Ganeshkhind, Pune University Campus, Pune, Maharashtra - 411007 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Mon Dec 12 2011 - 02:30:03 PST