Note that the C coefficient terms correspond to the C4 terms inside the prmtop file.
> On Sep 22, 2018, at 10:41 AM, Pengfei Li <ambermailpengfei.gmail.com> wrote:
>
> Hi Deepika,
>
> It seems the version of ParmEd you used did not print out the C coefficient.
>
> Please check the last several paragraphs of this tutorial: http://ambermd.org/tutorials/advanced/tutorial20/12_6_4.htm <http://ambermd.org/tutorials/advanced/tutorial20/12_6_4.htm>. For checking C4 parameters between ion and atom types which are not “OW”, you can check the equations 13 and 14 in this paper: https://pubs.acs.org/doi/pdfplus/10.1021/ct500918t <https://pubs.acs.org/doi/pdfplus/10.1021/ct500918t>, then compare the C4 values generated to the C4 values calculated by hand.
>
> Hope it helps,
> Pengfei
>
>> On Sep 16, 2018, at 12:33 PM, Deepika Sardana <dsardana92.gmail.com <mailto:dsardana92.gmail.com>> wrote:
>>
>> 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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org <mailto:AMBER.ambermd.org>
>> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sat Sep 22 2018 - 08:00:03 PDT
