Dear All,
while adding 12_6_4 Lennard Jones parameters for monovalent ions Na+ and
Cl- into prmtop file, using Parmed with following input file
LoadRestrt dna.inpcrd
SetOverwrite True
add12_6_4 .%Na+,Cl- watermodel SPCE
printLJMatrix :1
outparm 1264_modified.prmtop 1264_modified.inpcrd
it prints
***********************************************************
The selected metal ion is Na
The selected metal ion is Cl
Atom Type 1 Atom Type 2 A
coefficient B coefficient R i,j Eps i,j
------------------------------------------------------------------------------------------------------------------
HO [1] HO [1]
0.000000 0.000000 0.000000 0.000000
HO [1] OH [2]
0.000000 0.000000 0.000000 0.000000
HO [1] CI,CT [3]
0.000000 0.000000 0.000000 0.000000
HO [1] H1 [4]
0.000000 0.000000 0.000000 0.000000
HO [1] OS [5]
0.000000 0.000000 0.000000 0.000000
HO [1] H2 [6]
0.000000 0.000000 0.000000 0.000000
HO [1] N*,N2,NA,NB,NC [7]
0.000000 0.000000 0.000000 0.000000
HO [1] C,C*,CA,CB,CK,CM,CN,CQ,CW [8]
0.000000 0.000000 0.000000 0.000000
HO [1] H4 [9]
0.000000 0.000000 0.000000 0.000000
HO [1] HA [10]
0.000000 0.000000 0.000000 0.000000
HO [1] H [11]
0.000000 0.000000 0.000000 0.000000
HO [1] O,O2 [12]
0.000000 0.000000 0.000000 0.000000
HO [1] HC [13]
0.000000 0.000000 0.000000 0.000000
HO [1] P [14]
0.000000 0.000000 0.000000 0.000000
HO [1] H5 [15]
0.000000 0.000000 0.000000 0.000000
HO [1] Na+ [16]
0.000000 0.000000 0.000000 0.000000
HO [1] Cl- [17]
0.000000 0.000000 0.000000 0.000000
HO [1] OW [18]
0.000000 0.000000 0.000000 0.000000
HO [1] HW [19]
0.000000 0.000000 0.000000 0.000000
HO [1] OH [2]
0.000000 0.000000 0.000000 0.000000
OH [2] OH [2]
581803.229000 699.746810 3.442000 0.210400
OH [2] CI,CT [3]
791544.157000 693.079947 3.629000 0.151716
OH [2] H1 [4]
46692.251400 103.606917 3.108000 0.057474
OH [2] OS [5]
458874.091000 589.183300 3.404700 0.189124
OH [2] H2 [6]
31536.005100 85.147065 3.008000 0.057474
OH [2] N*,N2,NA,NB,NC [7]
744975.864000 750.714425 3.545000 0.189124
OH [2] C,C*,CA,CB,CK,CM,CN,CQ,CW [8]
701803.794000 614.502845 3.629000 0.134515
OH [2] H4 [9]
49670.730600 105.648788 3.130000 0.056178
OH [2] HA [10]
60075.021800 116.187983 3.180000 0.056178
OH [2] H [11]
1404.670230 17.970226 2.321000 0.057474
OH [2] O,O2 [12]
471003.287000 629.300710 3.382200 0.210200
OH [2] HC [13]
68278.663100 125.287818 3.208000 0.057474
OH [2] P [14]
1986837.360000 1276.821210 3.821000 0.205134
OH [2] H5 [15]
40942.758100 95.918591 3.080000 0.056178
OH [2] Na+ [16]
90566.183500 170.923804 3.193000 0.080645
OH [2] Cl- [17]
3794223.660000 2244.890830 3.874000 0.332053
OH [2] OW [18]
582511.344000 645.512297 3.489300 0.178832
OH [2] HW [19]
0.000000 0.000000 0.000000 0.000000
HO [1] CI,CT [3]
0.000000 0.000000 0.000000 0.000000
OH [2] CI,CT [3]
791544.157000 693.079947 3.629000 0.151716
CI,CT [3] CI,CT [3]
1043080.230000 675.612247 3.816000 0.109400
CI,CT [3] H1 [4]
67877.136800 106.076943 3.295000 0.041444
CI,CT [3] OS [5]
628541.240000 585.549272 3.591700 0.136374
CI,CT [3] H2 [6]
46893.088500 88.168542 3.195000 0.041444
CI,CT [3] N*,N2,NA,NB,NC [7]
995480.466000 736.907417 3.732000 0.136374
CI,CT [3] C,C*,CA,CB,CK,CM,CN,CQ,CW [8]
924822.270000 599.015525 3.816000 0.096997
CI,CT [3] H4 [9]
71862.107400 107.908863 3.317000 0.040509
CI,CT [3] HA [10]
85994.700300 118.043746 3.367000 0.040509
CI,CT [3] H [11]
2566.781340 20.627836 2.508000 0.041444
CI,CT [3] O,O2 [12]
647841.731000 626.720080 3.569200 0.151572
CI,CT [3] HC [13]
97170.811700 126.919150 3.395000 0.041444
CI,CT [3] P [14]
2541886.840000 1226.365520 4.008000 0.147919
CI,CT [3] H5 [15]
59888.564600 98.509722 3.267000 0.040509
CI,CT [3] Na+ [16]
129290.091000 173.418344 3.380000 0.058152
CI,CT [3] Cl- [17]
4817139.230000 2147.935610 4.061000 0.239438
CI,CT [3] OW [18]
785890.042000 636.687196 3.676300 0.128953
CI,CT [3] HW [19]
0.000000 0.000000 0.000000 0.000000
HO [1] H1 [4]
0.000000 0.000000 0.000000 0.000000
OH [2] H1 [4]
46692.251400 103.606917 3.108000 0.057474
CI,CT [3] H1 [4]
67877.136800 106.076943 3.295000 0.041444
H1 [4] H1 [4]
3259.696250 14.307653 2.774000 0.015700
H1 [4] OS [5]
36309.724600 86.622082 3.070700 0.051662
H1 [4] H2 [6]
2098.149780 11.478842 2.674000 0.015700
H1 [4] N*,N2,NA,NB,NC [7]
62066.599700 113.252061 3.211000 0.051662
H1 [4] C,C*,CA,CB,CK,CM,CN,CQ,CW [8]
60181.648400 94.050598 3.295000 0.036745
H1 [4] H4 [9]
3503.010670 14.663865 2.796000 0.015346
H1 [4] HA [10]
4333.254580 16.309281 2.846000 0.015346
H1 [4] H [11]
59.466730 1.932488 1.987000 0.015700
H1 [4] O,O2 [12]
36947.153000 92.119214 3.048200 0.057420
H1 [4] HC [13]
4985.868480 17.694986 2.874000 0.015700
H1 [4] P [14]
181087.383000 201.468199 3.487000 0.056036
H1 [4] H5 [15]
2820.991970 13.159175 2.746000 0.015346
H1 [4] Na+ [16]
6570.158800 24.061402 2.859000 0.022030
H1 [4] Cl- [17]
351296.347000 357.013022 3.540000 0.090706
H1 [4] OW [18]
47572.887200 96.415212 3.155300 0.048851
H1 [4] HW [19]
0.000000 0.000000 0.000000 0.000000
HO [1] OS [5]
0.000000 0.000000 0.000000 0.000000
OH [2] OS [5]
458874.091000 589.183300 3.404700 0.189124
CI,CT [3] OS [5]
628541.240000 585.549272 3.591700 0.136374
H1 [4] OS [5]
36309.724600 86.622082 3.070700 0.051662
OS [5] OS [5]
361397.723000 495.732238 3.367400 0.170000
OS [5] H2 [6]
24405.057900 71.016139 2.970700 0.051662
OS [5] N*,N2,NA,NB,NC [7]
589818.288000 633.305958 3.507700 0.170000
OS [5] C,C*,CA,CB,CK,CM,CN,CQ,CW [8]
557281.136000 519.163331 3.591700 0.120913
OS [5] H4 [9]
38665.499300 88.374476 3.092700 0.050498
OS [5] HA [10]
46871.105500 97.301075 3.142700 0.050498
OS [5] H [11]
1039.544080 14.656781 2.283700 0.051662
OS [5] O,O2 [12]
370622.491000 529.252520 3.344900 0.188944
OS [5] HC [13]
53337.925200 104.986921 3.170700 0.051662
OS [5] P [14]
1587595.280000 1082.105550 3.783700 0.184391
OS [5] H5 [15]
31796.528300 80.141025 3.042700 0.050498
OS [5] Na+ [16]
70701.585800 143.180835 3.155700 0.072490
OS [5] Cl- [17]
3036709.370000 1904.084300 3.836700 0.298476
OS [5] OW [18]
460252.016000 544.002597 3.452000 0.160748
OS [5] HW [19]
0.000000 0.000000 0.000000 0.000000
HO [1] H2 [6]
0.000000 0.000000 0.000000 0.000000
OH [2] H2 [6]
31536.005100 85.147065 3.008000 0.057474
CI,CT [3] H2 [6]
46893.088500 88.168542 3.195000 0.041444
H1 [4] H2 [6]
2098.149780 11.478842 2.674000 0.015700
OS [5] H2 [6]
24405.057900 71.016139 2.970700 0.051662
H2 [6] H2 [6]
1328.012500 9.132315 2.574000 0.015700
H2 [6] N*,N2,NA,NB,NC [7]
42459.455500 93.670826 3.111000 0.051662
H2 [6] C,C*,CA,CB,CK,CM,CN,CQ,CW [8]
41576.641200 78.172540 3.195000 0.036745
H2 [6] H4 [9]
2262.737160 11.785412 2.696000 0.015346
H2 [6] HA [10]
2820.991970 13.159175 2.746000 0.015346
H2 [6] H [11]
32.000919 1.417624 1.887000 0.015700
H2 [6] O,O2 [12]
24759.551600 75.410378 2.948200 0.057420
H2 [6] HC [13]
3259.696250 14.307653 2.774000 0.015700
H2 [6] P [14]
127716.552000 169.194406 3.387000 0.056036
H2 [6] H5 [15]
1807.480140 10.533301 2.646000 0.015346
H2 [6] Na+ [16]
4285.745800 19.433284 2.759000 0.022030
H2 [6] Cl- [17]
249078.247000 300.618111 3.440000 0.090706
H2 [6] OW [18]
32323.467300 79.473946 3.055300 0.048851
H2 [6] HW [19]
0.000000 0.000000 0.000000 0.000000
HO [1] N*,N2,NA,NB,NC [7]
0.000000 0.000000 0.000000 0.000000
OH [2] N*,N2,NA,NB,NC [7]
744975.864000 750.714425 3.545000 0.189124
CI,CT [3] N*,N2,NA,NB,NC [7]
995480.466000 736.907417 3.732000 0.136374
H1 [4] N*,N2,NA,NB,NC [7]
62066.599700 113.252061 3.211000 0.051662
OS [5] N*,N2,NA,NB,NC [7]
589818.288000 633.305958 3.507700 0.170000
H2 [6] N*,N2,NA,NB,NC [7]
42459.455500 93.670826 3.111000 0.051662
N*,N2,NA,NB,NC [7] N*,N2,NA,NB,NC [7]
944293.233000 801.323529 3.648000 0.170000
N*,N2,NA,NB,NC [7] C,C*,CA,CB,CK,CM,CN,CQ,CW [8]
882619.071000 653.361429 3.732000 0.120913
N*,N2,NA,NB,NC [7] H4 [9]
65847.387000 115.327881 3.233000 0.050498
N*,N2,NA,NB,NC [7] HA [10]
79162.715400 126.451907 3.283000 0.050498
N*,N2,NA,NB,NC [7] H [11]
2126.011810 20.960420 2.424000 0.051662
N*,N2,NA,NB,NC [7] O,O2 [12]
606829.342000 677.220874 3.485200 0.188944
N*,N2,NA,NB,NC [7] HC [13]
89677.698900 136.131731 3.311000 0.051662
N*,N2,NA,NB,NC [7] P [14]
2457465.580000 1346.304960 3.924000 0.184391
N*,N2,NA,NB,NC [7] H5 [15]
54614.725300 105.031585 3.183000 0.050498
N*,N2,NA,NB,NC [7] Na+ [16]
119159.061000 185.880508 3.296000 0.072490
N*,N2,NA,NB,NC [7] Cl- [17]
4672789.490000 2361.960690 3.977000 0.298476
N*,N2,NA,NB,NC [7] OW [18]
742364.908000 690.894667 3.592300 0.160748
N*,N2,NA,NB,NC [7] HW [19]
0.000000 0.000000 0.000000 0.000000
HO [1] C,C*,CA,CB,CK,CM,CN,CQ,CW [8]
0.000000 0.000000 0.000000 0.000000
OH [2] C,C*,CA,CB,CK,CM,CN,CQ,CW [8]
701803.794000 614.502845 3.629000 0.134515
CI,CT [3] C,C*,CA,CB,CK,CM,CN,CQ,CW [8]
924822.270000 599.015525 3.816000 0.096997
H1 [4] C,C*,CA,CB,CK,CM,CN,CQ,CW [8]
60181.648400 94.050598 3.295000 0.036745
OS [5] C,C*,CA,CB,CK,CM,CN,CQ,CW [8]
557281.136000 519.163331 3.591700 0.120913
H2 [6] C,C*,CA,CB,CK,CM,CN,CQ,CW [8]
41576.641200 78.172540 3.195000 0.036745
N*,N2,NA,NB,NC [7] C,C*,CA,CB,CK,CM,CN,CQ,CW [8]
882619.071000 653.361429 3.732000 0.120913
C,C*,CA,CB,CK,CM,CN,CQ,CW [8] C,C*,CA,CB,CK,CM,CN,CQ,CW [8]
819971.662000 531.102864 3.816000 0.086000
C,C*,CA,CB,CK,CM,CN,CQ,CW [8] H4 [9]
63714.827800 95.674826 3.317000 0.035917
C,C*,CA,CB,CK,CM,CN,CQ,CW [8] HA [10]
76245.155000 104.660679 3.367000 0.035917
C,C*,CA,CB,CK,CM,CN,CQ,CW [8] H [11]
2275.775610 18.289180 2.508000 0.036745
C,C*,CA,CB,CK,CM,CN,CQ,CW [8] O,O2 [12]
574393.458000 555.666448 3.569200 0.134387
C,C*,CA,CB,CK,CM,CN,CQ,CW [8] HC [13]
86154.188300 112.529845 3.395000 0.036745
C,C*,CA,CB,CK,CM,CN,CQ,CW [8] P [14]
2253703.490000 1087.327810 4.008000 0.131149
C,C*,CA,CB,CK,CM,CN,CQ,CW [8] H5 [15]
53098.771000 87.341301 3.267000 0.035917
C,C*,CA,CB,CK,CM,CN,CQ,CW [8] Na+ [16]
114631.983000 153.757249 3.380000 0.051559
C,C*,CA,CB,CK,CM,CN,CQ,CW [8] Cl- [17]
4271001.890000 1904.416000 4.061000 0.212292
C,C*,CA,CB,CK,CM,CN,CQ,CW [8] OW [18]
696790.708000 564.503554 3.676300 0.114333
C,C*,CA,CB,CK,CM,CN,CQ,CW [8] HW [19]
0.000000 0.000000 0.000000 0.000000
HO [1] H4 [9]
0.000000 0.000000 0.000000 0.000000
OH [2] H4 [9]
49670.730600 105.648788 3.130000 0.056178
CI,CT [3] H4 [9]
71862.107400 107.908863 3.317000 0.040509
H1 [4] H4 [9]
3503.010670 14.663865 2.796000 0.015346
OS [5] H4 [9]
38665.499300 88.374476 3.092700 0.050498
H2 [6] H4 [9]
2262.737160 11.785412 2.696000 0.015346
N*,N2,NA,NB,NC [7] H4 [9]
65847.387000 115.327881 3.233000 0.050498
C,C*,CA,CB,CK,CM,CN,CQ,CW [8] H4 [9]
63714.827800 95.674826 3.317000 0.035917
H4 [9] H4 [9]
3761.691050 15.023364 2.818000 0.015000
H4 [9] HA [10]
4645.591550 16.695373 2.868000 0.015000
H4 [9] H [11]
66.336827 2.017925 2.009000 0.015346
H4 [9] O,O2 [12]
39369.081700 94.012430 3.070200 0.056125
H4 [9] HC [13]
5340.453600 18.105762 2.896000 0.015346
H4 [9] P [14]
190880.272000 204.498832 3.509000 0.054772
H4 [9] H5 [15]
3034.480060 13.493287 2.768000 0.015000
H4 [9] Na+ [16]
7040.782120 24.625857 2.881000 0.021533
H4 [9] Cl- [17]
369876.956000 362.179429 3.562000 0.088661
H4 [9] OW [18]
50543.591300 98.253212 3.177300 0.047749
H4 [9] HW [19]
0.000000 0.000000 0.000000 0.000000
HO [1] HA [10]
0.000000 0.000000 0.000000 0.000000
OH [2] HA [10]
60075.021800 116.187983 3.180000 0.056178
CI,CT [3] HA [10]
85994.700300 118.043746 3.367000 0.040509
H1 [4] HA [10]
4333.254580 16.309281 2.846000 0.015346
OS [5] HA [10]
46871.105500 97.301075 3.142700 0.050498
H2 [6] HA [10]
2820.991970 13.159175 2.746000 0.015346
N*,N2,NA,NB,NC [7] HA [10]
79162.715400 126.451907 3.283000 0.050498
C,C*,CA,CB,CK,CM,CN,CQ,CW [8] HA [10]
76245.155000 104.660679 3.367000 0.035917
H4 [9] HA [10]
4645.591550 16.695373 2.868000 0.015000
HA [10] HA [10]
5716.296010 18.519659 2.918000 0.015000
HA [10] H [11]
89.098751 2.338641 2.059000 0.015346
HA [10] O,O2 [12]
47790.818300 103.580945 3.120200 0.056125
HA [10] HC [13]
6558.256010 20.064203 2.946000 0.015346
HA [10] P [14]
226202.022000 222.617115 3.559000 0.054772
HA [10] H5 [15]
3761.691050 15.023364 2.818000 0.015000
HA [10] Na+ [16]
8655.489370 27.304028 2.931000 0.021533
HA [10] Cl- [17]
437223.194000 393.773729 3.612000 0.088661
HA [10] OW [18]
60959.230900 107.902982 3.227300 0.047749
HA [10] HW [19]
0.000000 0.000000 0.000000 0.000000
HO [1] H [11]
0.000000 0.000000 0.000000 0.000000
OH [2] H [11]
1404.670230 17.970226 2.321000 0.057474
CI,CT [3] H [11]
2566.781340 20.627836 2.508000 0.041444
H1 [4] H [11]
59.466730 1.932488 1.987000 0.015700
OS [5] H [11]
1039.544080 14.656781 2.283700 0.051662
H2 [6] H [11]
32.000919 1.417624 1.887000 0.015700
N*,N2,NA,NB,NC [7] H [11]
2126.011810 20.960420 2.424000 0.051662
C,C*,CA,CB,CK,CM,CN,CQ,CW [8] H [11]
2275.775610 18.289180 2.508000 0.036745
H4 [9] H [11]
66.336827 2.017925 2.009000 0.015346
HA [10] H [11]
89.098751 2.338641 2.059000 0.015346
H [11] H [11]
0.139983 0.093760 1.200000 0.015700
H [11] O,O2 [12]
1025.952360 15.350528 2.261200 0.057420
H [11] HC [13]
107.193646 2.594564 2.087000 0.015700
H [11] P [14]
8410.658390 43.418759 2.700000 0.056036
H [11] H5 [15]
49.023994 1.734731 1.959000 0.015346
H [11] Na+ [16]
137.937711 3.486378 2.072000 0.022030
H [11] Cl- [17]
17191.312200 78.977204 2.753000 0.090706
H [11] OW [18]
1520.940410 17.239390 2.368300 0.048851
H [11] HW [19]
0.000000 0.000000 0.000000 0.000000
HO [1] O,O2 [12]
0.000000 0.000000 0.000000 0.000000
OH [2] O,O2 [12]
471003.287000 629.300710 3.382200 0.210200
CI,CT [3] O,O2 [12]
647841.731000 626.720080 3.569200 0.151572
H1 [4] O,O2 [12]
36947.153000 92.119214 3.048200 0.057420
OS [5] O,O2 [12]
370622.491000 529.252520 3.344900 0.188944
H2 [6] O,O2 [12]
24759.551600 75.410378 2.948200 0.057420
N*,N2,NA,NB,NC [7] O,O2 [12]
606829.342000 677.220874 3.485200 0.188944
C,C*,CA,CB,CK,CM,CN,CQ,CW [8] O,O2 [12]
574393.458000 555.666448 3.569200 0.134387
H4 [9] O,O2 [12]
39369.081700 94.012430 3.070200 0.056125
HA [10] O,O2 [12]
47790.818300 103.580945 3.120200 0.056125
H [11] O,O2 [12]
1025.952360 15.350528 2.261200 0.057420
O,O2 [12] O,O2 [12]
379876.399000 564.885984 3.322400 0.210000
O,O2 [12] HC [13]
54426.104200 111.805549 3.148200 0.057420
O,O2 [12] P [14]
1642637.660000 1160.414660 3.761200 0.204939
O,O2 [12] H5 [15]
32328.363100 85.192133 3.020200 0.056125
O,O2 [12] Na+ [16]
72114.606500 152.448981 3.133200 0.080569
O,O2 [12] Cl- [17]
3145110.100000 2042.890450 3.814200 0.331737
O,O2 [12] OW [18]
472934.643000 581.361517 3.429500 0.178662
O,O2 [12] HW [19]
0.000000 0.000000 0.000000 0.000000
HO [1] HC [13]
0.000000 0.000000 0.000000 0.000000
OH [2] HC [13]
68278.663100 125.287818 3.208000 0.057474
CI,CT [3] HC [13]
97170.811700 126.919150 3.395000 0.041444
H1 [4] HC [13]
4985.868480 17.694986 2.874000 0.015700
OS [5] HC [13]
53337.925200 104.986921 3.170700 0.051662
H2 [6] HC [13]
3259.696250 14.307653 2.774000 0.015700
N*,N2,NA,NB,NC [7] HC [13]
89677.698900 136.131731 3.311000 0.051662
C,C*,CA,CB,CK,CM,CN,CQ,CW [8] HC [13]
86154.188300 112.529845 3.395000 0.036745
H4 [9] HC [13]
5340.453600 18.105762 2.896000 0.015346
HA [10] HC [13]
6558.256010 20.064203 2.946000 0.015346
H [11] HC [13]
107.193646 2.594564 2.087000 0.015700
O,O2 [12] HC [13]
54426.104200 111.805549 3.148200 0.057420
HC [13] HC [13]
7516.077030 21.725783 2.974000 0.015700
HC [13] P [14]
254238.516000 238.716853 3.587000 0.056036
HC [13] H5 [15]
4333.254580 16.309281 2.846000 0.015346
HC [13] Na+ [16]
9925.344380 29.573709 2.959000 0.022030
HC [13] Cl- [17]
490739.588000 421.961461 3.640000 0.090706
HC [13] OW [18]
69177.336800 116.264660 3.255300 0.048851
HC [13] HW [19]
0.000000 0.000000 0.000000 0.000000
Outputting Amber topology file 1264_modified.prmtop and restart
1264_modified.inpcrd
Done!
My Question is how to determine whether the added parameters are correct or
not?
Thanks
Deepika Sardana
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Received on Sun Sep 16 2018 - 10:00:02 PDT
