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, Francois
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
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Received on Mon Dec 12 2011 - 02:00:03 PST
