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fix Charmm NBThole calculation bug and Improper dihedral parameter match issue (#2952)  
qiuzy committed
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* GENERATE PSF WITH OPTIMIZED
* DRUDE PROTEIN FORCE FIELD
*  DATE:    12/18/20     21: 0:51      CREATED BY USER: qiuzy
*
       176  EXT
         1         1  CYT       H5T             9.2932028107       10.8307655966       18.0403805565  DNA       1               0.0000000000
         2         1  CYT       O5'             9.7405057857       10.9593876058       17.1900208161  DNA       1               0.0000000000
         3         1  CYT       DO5'            9.7443608855       10.9701534822       17.2167747416  DNA       1               0.0000000000
         4         1  CYT       C5'             9.3378314770        9.8642782612       16.3526854601  DNA       1               0.0000000000
         5         1  CYT       DC5'            9.3228652453        9.8708543183       16.3690757578  DNA       1               0.0000000000
         6         1  CYT       H5'             8.2433627306        9.8918886167       16.1409964005  DNA       1               0.0000000000
         7         1  CYT       H5''            9.6966975882        8.8884478625       16.7528768866  DNA       1               0.0000000000
         8         1  CYT       LP5A           10.0329938722       10.8762904825       17.3633574304  DNA       1               0.0000000000
         9         1  CYT       LP5B            9.5216068682       11.2291939395       17.1477383635  DNA       1               0.0000000000
        10         1  CYT       N1             10.7047933306       13.5599274596       14.7217834187  DNA       1               0.0000000000
        11         1  CYT       DN1            10.7171602569       13.6006466854       14.9192228159  DNA       1               0.0000000000
        12         1  CYT       C6             10.8458690961       13.7526817274       16.0576344359  DNA       1               0.0000000000
        13         1  CYT       DC6            10.8742308520       13.8393255725       16.2925497977  DNA       1               0.0000000000
        14         1  CYT       H6             11.0900286235       12.8603303781       16.6355660785  DNA       1               0.0000000000
        15         1  CYT       C2             10.4015820054       14.6360827853       13.9005309947  DNA       1               0.0000000000
        16         1  CYT       DC2            10.4344031214       14.4646101275       13.8938155983  DNA       1               0.0000000000
        17         1  CYT       O2             10.2742291657       14.4537442986       12.6812447655  DNA       1               0.0000000000
        18         1  CYT       DO2            10.2610055335       14.5122753146       12.6878191455  DNA       1               0.0000000000
        19         1  CYT       LP2A           10.1984600236       14.7561982490       12.5222459092  DNA       1               0.0000000000
        20         1  CYT       LP2B           10.3278830615       14.1165289212       12.6043873723  DNA       1               0.0000000000
        21         1  CYT       N3             10.2435796272       15.8610716979       14.4576865192  DNA       1               0.0000000000
        22         1  CYT       DN3            10.2437225105       15.8053678902       14.3999071713  DNA       1               0.0000000000
        23         1  CYT       LP3            10.1648888158       16.1402345268       14.2617889112  DNA       1               0.0000000000
        24         1  CYT       C4             10.3889844094       16.0095613165       15.7699689627  DNA       1               0.0000000000
        25         1  CYT       DC4            10.3689407643       16.0448179651       15.6964577735  DNA       1               0.0000000000
        26         1  CYT       N4             10.2283490971       17.2280334028       16.3036245770  DNA       1               0.0000000000
        27         1  CYT       DN4            10.2227494101       17.2231155259       16.3074327496  DNA       1               0.0000000000
        28         1  CYT       H41            10.0031070134       18.0034261022       15.6923653660  DNA       1               0.0000000000
        29         1  CYT       H42            10.3330975496       17.3759830496       17.2998472449  DNA       1               0.0000000000
        30         1  CYT       C5             10.7021146086       14.9326311974       16.6125891448  DNA       1               0.0000000000
        31         1  CYT       DC5            10.6453773081       15.1266438450       16.5340012782  DNA       1               0.0000000000
        32         1  CYT       H5             10.8113110875       15.0954944323       17.6785470341  DNA       1               0.0000000000
        33         1  CYT       C4'            10.0035522446       10.0080707962       14.9870200987  DNA       1               0.0000000000
        34         1  CYT       DC4'            9.9902769466       10.0171203034       15.0014752810  DNA       1               0.0000000000
        35         1  CYT       H4'             9.6476214004        9.2236148313       14.3044738544  DNA       1               0.0000000000
        36         1  CYT       O4'             9.6512896821       11.2937564245       14.4216418735  DNA       1               0.0000000000
        37         1  CYT       DO4'            9.6440196904       11.3024029738       14.4049072086  DNA       1               0.0000000000
        38         1  CYT       LPRA            9.4961560382       11.4451319342       14.6964490800  DNA       1               0.0000000000
        39         1  CYT       LPRB            9.5814265433       11.2022962211       14.0911056684  DNA       1               0.0000000000
        40         1  CYT       LPX             9.7452677830       11.2687306852       14.4449190658  DNA       1               0.0000000000
        41         1  CYT       C1'            10.8929563473       12.1549888049       14.2510602770  DNA       1               0.0000000000
        42         1  CYT       DC1'           10.8869695971       12.1749540876       14.3150932056  DNA       1               0.0000000000
        43         1  CYT       H1'            11.1148810267       12.1990133142       13.1737975513  DNA       1               0.0000000000
        44         1  CYT       C2'            11.9986965375       11.4386489370       14.9958450658  DNA       1               0.0000000000
        45         1  CYT       DC2'           11.9603418629       11.4091724259       14.9717319705  DNA       1               0.0000000000
        46         1  CYT       H2''           12.0887188971       11.8273479133       16.0182936981  DNA       1               0.0000000000
        47         1  CYT       H2'            12.9011995827       11.5889332288       14.4182512845  DNA       1               0.0000000000
        48         1  CYT       C3'            11.5288612740       10.0002924476       15.0123701837  DNA       1               0.0000000000
        49         1  CYT       DC3'           11.4149102348        9.9714169074       15.0447839793  DNA       1               0.0000000000
        50         1  CYT       H3'            11.9181626566        9.5626986208       15.9340285594  DNA       1               0.0000000000
        51         1  CYT       O3'            12.1192972201        9.2744376379       13.9250283861  DNA       1               0.0000000000
        52         1  CYT       DO3'           12.1261589188        9.2661927690       13.9105780491  DNA       1               0.0000000000
        53         2  GUA       P              13.6126892952        9.6666210188       13.4629397870  DNA       2               0.0000000000
        54         2  GUA       DP             13.5974540487        9.6533261933       13.4695461097  DNA       2               0.0000000000
        55         2  GUA       O1P            14.3391933902       10.3706743189       14.5560757832  DNA       2               0.0000000000
        56         2  GUA       DO1P           14.3130879412       10.3755078794       14.5483045279  DNA       2               0.0000000000
        57         2  GUA       O2P            14.2928034370        8.4583505968       12.9560628695  DNA       2               0.0000000000
        58         2  GUA       DO2P           14.2601877114        8.4431802852       12.9519335310  DNA       2               0.0000000000
        59         2  GUA       O5'            13.2927290918       10.6646658107       12.2542919090  DNA       2               0.0000000000
        60         2  GUA       DO5'           13.3001859458       10.6516009153       12.2945931388  DNA       2               0.0000000000
        61         2  GUA       C5'            12.3255169585       10.2802735866       11.2592370529  DNA       2               0.0000000000
        62         2  GUA       DC5'           12.2784190645       10.3146328091       11.1969012214  DNA       2               0.0000000000
        63         2  GUA       H5'            11.3455988541       10.7637231239       11.4848189715  DNA       2               0.0000000000
        64         2  GUA       H5''           12.3132363236        9.1724445338       11.1579130414  DNA       2               0.0000000000
        65         2  GUA       N9             14.2853219132       13.7140499534       10.7654868469  DNA       2               0.0000000000
        66         2  GUA       DN9            14.2899554574       13.7172067956       10.7816395213  DNA       2               0.0000000000
        67         2  GUA       C4             14.1524568617       15.0605474808       10.5730753810  DNA       2               0.0000000000
        68         2  GUA       DC4            14.1649106805       15.0054544872       10.5752232966  DNA       2               0.0000000000
        69         2  GUA       N3             13.7491120066       15.6815990748        9.4421527763  DNA       2               0.0000000000
        70         2  GUA       DN3            13.7360685150       15.7529761787        9.4097745025  DNA       2               0.0000000000
        71         2  GUA       LP3            13.6587790568       15.5177332886        9.1463691374  DNA       2               0.0000000000
        72         2  GUA       C2             13.7302328868       17.0003966115        9.5701584905  DNA       2               0.0000000000
        73         2  GUA       DC2            13.7227402073       17.0046526985        9.5511129244  DNA       2               0.0000000000
        74         2  GUA       N1             14.0807487539       17.6732976817       10.7201620363  DNA       2               0.0000000000
        75         2  GUA       DN1            14.0627115270       17.6465944960       10.6619374053  DNA       2               0.0000000000
        76         2  GUA       H1             14.0287779671       18.6927448983       10.7075555782  DNA       2               0.0000000000
        77         2  GUA       N2             13.3503674517       17.7614398450        8.5335320211  DNA       2               0.0000000000
        78         2  GUA       DN2            13.3553271002       17.7713609867        8.5668692806  DNA       2               0.0000000000
        79         2  GUA       H21            13.2968624269       18.7727575459        8.5124912562  DNA       2               0.0000000000
        80         2  GUA       H22            13.0920597792       17.2727798656        7.6846907042  DNA       2               0.0000000000
        81         2  GUA       C6             14.5003198368       17.0563104684       11.8976081222  DNA       2               0.0000000000
        82         2  GUA       DC6            14.5259159765       17.0987750347       11.9785124763  DNA       2               0.0000000000
        83         2  GUA       O6             14.7956844322       17.7477450787       12.8829408850  DNA       2               0.0000000000
        84         2  GUA       DO6            14.7917319313       17.8061191042       12.8767425584  DNA       2               0.0000000000
        85         2  GUA       LP6A           14.8934339064       17.5419459565       13.1486321131  DNA       2               0.0000000000
        86         2  GUA       LP6B           14.7551520534       18.0871117248       12.8075261572  DNA       2               0.0000000000
        87         2  GUA       C5             14.5278071260       15.6568038635       11.7877178782  DNA       2               0.0000000000
        88         2  GUA       DC5            14.5000396903       15.7508093104       11.7051855005  DNA       2               0.0000000000
        89         2  GUA       N7             14.8797436890       14.6807561178       12.7083471274  DNA       2               0.0000000000
        90         2  GUA       DN7            14.8766912897       14.7103509970       12.7044716189  DNA       2               0.0000000000
        91         2  GUA       LP7            14.9882728859       14.7142830797       13.0394020363  DNA       2               0.0000000000
        92         2  GUA       C8             14.7192773375       13.5467101380       12.0659958660  DNA       2               0.0000000000
        93         2  GUA       DC8            14.7425557965       13.5929339133       12.1054368597  DNA       2               0.0000000000
        94         2  GUA       H8             14.9033162906       12.5596516591       12.4860473455  DNA       2               0.0000000000
        95         2  GUA       C4'            12.7277309043       10.8108599613        9.8877167788  DNA       2               0.0000000000
        96         2  GUA       DC4'           12.7438817170       10.8346838104        9.8877710838  DNA       2               0.0000000000
        97         2  GUA       H4'            11.9506671233       10.5889220202        9.1461387754  DNA       2               0.0000000000
        98         2  GUA       O4'            12.8557684975       12.2504316438        9.9686210551  DNA       2               0.0000000000
        99         2  GUA       DO4'           12.8507403809       12.2808297908        9.9532822079  DNA       2               0.0000000000
       100         2  GUA       LPRA           12.8404675862       12.3077460638       10.3135570415  DNA       2               0.0000000000
       101         2  GUA       LPRB           12.7025076665       12.3560597038        9.6722195786  DNA       2               0.0000000000
       102         2  GUA       LPX            12.9261747260       12.1823726023        9.9483486197  DNA       2               0.0000000000
       103         2  GUA       C1'            14.0283796572       12.6802528899        9.7487568163  DNA       2               0.0000000000
       104         2  GUA       DC1'           14.0390432208       12.6774344674        9.7732426765  DNA       2               0.0000000000
       105         2  GUA       H1'            13.9472002408       13.1109923452        8.7500546339  DNA       2               0.0000000000
       106         2  GUA       C2'            14.9588835678       11.4939001558        9.7907882024  DNA       2               0.0000000000
       107         2  GUA       DC2'           14.9289493218       11.4779058946        9.7551466797  DNA       2               0.0000000000
       108         2  GUA       H2''           15.3190287466       11.3600063764       10.8263915554  DNA       2               0.0000000000
       109         2  GUA       H2'            15.7594485925       11.6898635537        9.0692736025  DNA       2               0.0000000000
       110         2  GUA       C3'            14.0778992403       10.3185542158        9.3800840181  DNA       2               0.0000000000
       111         2  GUA       DC3'           13.9889255398       10.3232402275        9.4205990746  DNA       2               0.0000000000
       112         2  GUA       H3'            14.4074286571        9.4078482179        9.8880277398  DNA       2               0.0000000000
       113         2  GUA       O3'            14.0980339496       10.0296238206        7.9690998225  DNA       2               0.0000000000
       114         2  GUA       DO3'           14.1146819989       10.0448192638        7.9505848037  DNA       2               0.0000000000
       115         3  CYT       P              15.4966170410       10.0938838835        7.1918910281  DNA       3               0.0000000000
       116         3  CYT       DP             15.4836399688       10.1031335338        7.1847270552  DNA       3               0.0000000000
       117         3  CYT       O1P            16.6229278056        9.9925107749        8.1513568435  DNA       3               0.0000000000
       118         3  CYT       DO1P           16.6111838437       10.0044139080        8.1425933569  DNA       3               0.0000000000
       119         3  CYT       O2P            15.4906389094        9.1079356850        6.0839560838  DNA       3               0.0000000000
       120         3  CYT       DO2P           15.4765392685        9.1239667455        6.0776773089  DNA       3               0.0000000000
       121         3  CYT       O5'            15.4346054024       11.5733075922        6.5847093535  DNA       3               0.0000000000
       122         3  CYT       DO5'           15.4519788279       11.5678505389        6.5887656871  DNA       3               0.0000000000
       123         3  CYT       C5'            14.2338598934       12.0130780210        5.9257131423  DNA       3               0.0000000000
       124         3  CYT       DC5'           14.2111689293       12.1030513281        5.8671113193  DNA       3               0.0000000000
       125         3  CYT       H5'            13.6204792008       12.6218050524        6.6309700635  DNA       3               0.0000000000
       126         3  CYT       H5''           13.7239592375       11.1436712533        5.4556045276  DNA       3               0.0000000000
       127         3  CYT       N1             17.3708056866       14.4608685106        6.0097116886  DNA       3               0.0000000000
       128         3  CYT       DN1            17.4203492444       14.3553473746        6.1074347207  DNA       3               0.0000000000
       129         3  CYT       C6             17.7486704262       13.3834882119        6.7507287024  DNA       3               0.0000000000
       130         3  CYT       DC6            17.8422204842       13.2485891489        6.8625115562  DNA       3               0.0000000000
       131         3  CYT       H6             17.3551904410       12.4227311459        6.4178716941  DNA       3               0.0000000000
       132         3  CYT       C2             17.8125111743       15.7276359939        6.3606523658  DNA       3               0.0000000000
       133         3  CYT       DC2            17.7393456039       15.6861706337        6.2507192796  DNA       3               0.0000000000
       134         3  CYT       O2             17.4582142016       16.7029252059        5.6833800347  DNA       3               0.0000000000
       135         3  CYT       DO2            17.4823852380       16.7291225596        5.7093687830  DNA       3               0.0000000000
       136         3  CYT       LP2A           17.5969375809       16.9963582397        5.8143489998  DNA       3               0.0000000000
       137         3  CYT       LP2B           17.2497034812       16.5981279767        5.4225336730  DNA       3               0.0000000000
       138         3  CYT       N3             18.6268101784       15.8622185658        7.4350789294  DNA       3               0.0000000000
       139         3  CYT       DN3            18.5947384591       15.8784239185        7.3885152736  DNA       3               0.0000000000
       140         3  CYT       LP3            18.7463878437       16.1762493490        7.5329862820  DNA       3               0.0000000000
       141         3  CYT       C4             18.9802228242       14.7868435055        8.1320599344  DNA       3               0.0000000000
       142         3  CYT       DC4            18.9870091079       14.8585067416        8.1229937342  DNA       3               0.0000000000
       143         3  CYT       N4             19.7864744345       14.9401995876        9.1898012835  DNA       3               0.0000000000
       144         3  CYT       DN4            19.7866937645       14.9393993105        9.1808664532  DNA       3               0.0000000000
       145         3  CYT       H41            20.1033764306       15.8712950208        9.4324417474  DNA       3               0.0000000000
       146         3  CYT       H42            20.0743759378       14.1414660314        9.7422126367  DNA       3               0.0000000000
       147         3  CYT       C5             18.5390480055       13.5009015570        7.7916740087  DNA       3               0.0000000000
       148         3  CYT       DC5            18.6209207426       13.6671676446        7.8694584559  DNA       3               0.0000000000
       149         3  CYT       H5             18.8495836014       12.6474195141        8.3854454556  DNA       3               0.0000000000
       150         3  CYT       C4'            14.5722314767       12.9565858746        4.7755511076  DNA       3               0.0000000000
       151         3  CYT       DC4'           14.6194174088       12.9635294021        4.7584711128  DNA       3               0.0000000000
       152         3  CYT       H4'            13.6560182500       13.3575640701        4.3237067537  DNA       3               0.0000000000
       153         3  CYT       O4'            15.3257382340       14.0751333230        5.3008850585  DNA       3               0.0000000000
       154         3  CYT       DO4'           15.3477066283       14.1106197174        5.2926783427  DNA       3               0.0000000000
       155         3  CYT       LPRA           15.3993012990       13.9694635208        5.6263422485  DNA       3               0.0000000000
       156         3  CYT       LPRB           15.1827201512       14.3469961423        5.1331459238  DNA       3               0.0000000000
       157         3  CYT       LPX            15.3547485097       14.0057166575        5.2350084152  DNA       3               0.0000000000
       158         3  CYT       C1'            16.5090637148       14.1652005249        4.8501869155  DNA       3               0.0000000000
       159         3  CYT       DC1'           16.5394182353       14.1052888689        4.8817584318  DNA       3               0.0000000000
       160         3  CYT       H1'            16.4432368719       15.0044008711        4.1578092390  DNA       3               0.0000000000
       161         3  CYT       C2'            16.8215342471       12.8624066509        4.1409839134  DNA       3               0.0000000000
       162         3  CYT       DC2'           16.8128948543       12.8643513095        4.1128661256  DNA       3               0.0000000000
       163         3  CYT       H2''           17.2662180915       12.1629946284        4.8704358638  DNA       3               0.0000000000
       164         3  CYT       H2'            17.4790335660       13.0958740418        3.2958046285  DNA       3               0.0000000000
       165         3  CYT       C3'            15.4585303431       12.3528659759        3.6925173585  DNA       3               0.0000000000
       166         3  CYT       DC3'           15.4514728155       12.3606673045        3.6595919964  DNA       3               0.0000000000
       167         3  CYT       H3'            15.4458356826       11.2592702770        3.7034164728  DNA       3               0.0000000000
       168         3  CYT       O3'            15.0970628016       12.7444525649        2.3568327224  DNA       3               0.0000000000
       169         3  CYT       DO3'           15.0957402485       12.7465137953        2.3513381103  DNA       3               0.0000000000
       170         3  CYT       H3T            15.7208194811       12.3189037559        1.7477869821  DNA       3               0.0000000000
       171         3  CYT       LP3A           14.8631284962       12.5197425709        2.2253786739  DNA       3               0.0000000000
       172         3  CYT       LP3B           15.2621617862       13.0406278765        2.2701003881  DNA       3               0.0000000000
       173         4  SOD       SOD             8.0012643510        8.0008164757        3.0004178332  SOD       1               0.0000000000
       174         4  SOD       DSOD            7.9995263949        7.9996931111        2.9998442918  SOD       1               0.0000000000
       175         5  SOD       SOD            12.0044661566        5.0069237907       13.0004600645  SOD       2               0.0000000000
       176         5  SOD       DSOD           11.9983799335        4.9975433225       12.9998323610  SOD       2               0.0000000000