GROMACS version: 2021
GROMACS modification: Yes/No
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Hi dear friends. during use from ligand.prm file generated with swissparm i get many error, what is causes and how solve this? below i upload prm file content:
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- Built parameters for REC.mol2
- by user vzoete Mon Feb 1 21:26:10 UTC 2021
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BONDS
NC=O CR 335.651 1.4360
NC=O C=O 419.491 1.3690
NC=O HNCO 479.511 1.0150
NC=C CB 443.888 1.3980
NC=C CR 354.218 1.4460
NC=C HNCO 473.250 1.0180
NPYD CB 412.870 1.3330
N=C CB 397.901 1.3930
N=C C=O 725.204 1.2900
NC=C C=O 439.714 1.3700
NC=O OR 430.502 1.4100
CR CR 306.432 1.5080
CR C=O 301.539 1.4920
CR OR 363.214 1.4180
CR HCMM 342.991 1.0930
C=O OR 417.476 1.3550
C=O O=C 931.963 1.2220
C=O CB 322.985 1.4570
CB CB 401.068 1.3740
CR CB 356.737 1.4860
CB HCMM 381.853 1.0840
OR HOR 560.905 0.9720
OR HOCO 532.766 0.9810
ANGLES
CB NPYD CB 78.083 115.4060
C=O NC=O C=O 51.024 120.2740
C=O NC=O HNCO 41.380 120.2770
CB N=C C=O 85.279 111.6630
CB CB CB 48.145 119.9770
CB CB C=O 57.429 114.4750
CB CB NC=C 75.204 121.6330
CB CB HCMM 40.517 120.5710
NPYD CB CB 42.892 126.1390
NPYD CB CR 71.390 118.4320
CB CB CR 57.788 120.4190
NPYD CB C=O 79.810 112.7240
NPYD CB HCMM 49.872 115.5880
NPYD CB N=C 81.825 117.5910
N=C CB CB 70.095 121.0030
NC=O C=O CB 79.234 112.4950
NC=O C=O O=C 65.273 127.1520
CB C=O O=C 52.823 119.9680
NC=O C=O N=C 79.522 120.6970
NC=O C=O NC=C 78.658 119.6970
N=C C=O NC=C 60.739 128.0780
CR NC=O C=O 59.084 119.6000
CR NC=O HNCO 39.725 120.0660
CB NC=C CR 60.091 107.3490
CB NC=C HNCO 47.641 110.2880
CR NC=C HNCO 49.584 112.3740
C=O NC=C HNCO 50.376 114.8080
HNCO NC=C HNCO 40.301 109.1600
C=O NC=O OR 69.087 110.1330
OR NC=O HNCO 59.660 113.2140
CR CR C=O 55.917 107.5170
CR CR OR 71.390 108.1330
CR CR HCMM 45.770 110.5490
C=O CR OR 37.998 104.1120
C=O CR HCMM 46.778 108.3850
OR CR HCMM 56.205 108.5770
HCMM CR HCMM 37.134 108.8360
CR C=O OR 75.060 109.7160
CR C=O O=C 67.504 124.4100
OR C=O O=C 83.120 124.4250
NC=O CR CR 75.564 109.9600
NC=O CR C=O 45.626 102.6550
NC=O CR HCMM 53.255 107.6460
CR CR CR 61.243 109.6080
CB CR NC=C 81.249 109.1880
CB CR HCMM 45.122 109.4910
NC=C CR HCMM 51.743 109.8700
NC=O C=O CR 70.814 112.7350
OR CR OR 83.192 111.3680
CR OR HOR 57.069 106.5030
C=O OR CR 66.424 108.0550
C=O OR HOCO 41.956 111.9480
NC=O OR CR 119.175 105.3170
DIHEDRALS
NPYD CB CB NPYD 3.500 2 180.00
NPYD CB CB HCMM 3.500 2 180.00
NPYD CB CR NC=C 0.100 3 0.00
NPYD CB CR HCMM 0.100 3 0.00
NPYD CB CB N=C 3.500 2 180.00
NPYD CB C=O NC=O 1.250 2 180.00
NPYD CB C=O O=C 1.250 2 180.00
NPYD CB CB CR 3.500 2 180.00
NPYD CB N=C C=O 0.900 2 180.00
NPYD CB CB C=O 3.500 2 180.00
NC=O C=O CB CB 1.250 2 180.00
NC=O C=O N=C CB 8.000 2 180.00
NC=O C=O NC=C HNCO 1.950 2 180.00
N=C CB NPYD CB 0.000 1 0.00
N=C CB CB C=O 1.000 2 180.00
N=C C=O NC=O C=O 3.000 2 180.00
N=C C=O NC=O HNCO 3.000 2 180.00
N=C C=O NC=C HNCO 0.748 1 0.00
N=C C=O NC=C HNCO 2.184 2 180.00
N=C C=O NC=C HNCO -0.208 3 0.00
CB CB CB CB 3.500 2 180.00
CB CB CB HCMM 3.500 2 180.00
CB C=O NC=O CR 3.000 2 180.00
CB C=O NC=O HNCO 3.000 2 180.00
CB NC=C CR CB 0.125 3 0.00
CB NC=C CR HCMM 0.165 3 0.00
CB CB C=O O=C 1.250 2 180.00
CB CB CB NC=C 3.500 2 180.00
CB CB NC=C CR 2.168 2 180.00
CB CB NC=C CR 0.185 3 0.00
CB CB NC=C HNCO 0.357 1 0.00
CB CB NC=C HNCO 1.314 2 180.00
CB CB NC=C HNCO 1.677 3 0.00
CB CB CB C=O 3.500 2 180.00
CB NPYD CB CB 3.500 2 180.00
CB NPYD CB C=O 3.500 2 180.00
CB CR NC=C HNCO 0.125 3 0.00
CB NPYD CB CR 3.500 2 180.00
CB CB N=C C=O 0.900 2 180.00
CB C=O NC=O C=O 3.000 2 180.00
CB CB CR NC=C 0.100 3 0.00
CB CB CR HCMM -0.210 2 180.00
CB CB CR HCMM 0.196 3 0.00
CB NPYD CB HCMM 3.500 2 180.00
CB N=C C=O NC=C 0.900 2 180.00
C=O NC=O C=O NC=C 3.000 2 180.00
C=O NC=O C=O O=C 0.388 1 0.00
C=O NC=O C=O O=C -0.292 2 180.00
C=O NC=O C=O O=C -0.072 3 0.00
NC=O CR CR CR 0.150 3 0.00
NC=O CR CR HCMM 0.213 3 0.00
NC=O CR C=O OR 0.200 2 180.00
NC=O CR C=O OR 0.150 3 0.00
NC=O CR C=O O=C 0.169 1 0.00
NC=O CR C=O O=C 1.386 2 180.00
NC=O CR C=O O=C 1.073 3 0.00
NC=C CB CB HCMM 3.500 2 180.00
NC=C C=O NC=O HNCO 3.000 2 180.00
NC=O C=O CR CR -0.464 1 0.00
NC=O C=O CR CR 0.556 2 180.00
NC=O C=O CR CR 0.694 3 0.00
NC=O C=O CR HCMM -0.206 1 0.00
NC=O C=O CR HCMM 0.346 2 180.00
NC=O C=O CR HCMM 0.043 3 0.00
NC=O OR CR CR 0.100 3 0.00
NC=O OR CR HCMM 0.100 3 0.00
CR C=O OR CR -0.622 1 0.00
CR C=O OR CR 2.741 2 180.00
CR C=O OR CR 0.182 3 0.00
CR CR C=O OR -0.059 1 0.00
CR CR C=O OR -0.167 2 180.00
CR CR C=O OR 0.101 3 0.00
CR CR C=O O=C 0.412 1 0.00
CR CR C=O O=C 0.070 2 180.00
CR CR C=O O=C 0.163 3 0.00
CR CR OR HOR 0.135 2 180.00
CR CR OR HOR 0.118 3 0.00
C=O CR CR HCMM -0.128 1 0.00
C=O CR CR HCMM 0.029 2 180.00
C=O CR OR HOR -0.826 1 0.00
C=O CR OR HOR -0.830 2 180.00
C=O CR OR HOR 0.141 3 0.00
C=O OR CR CR -0.274 1 0.00
C=O OR CR CR 0.160 3 0.00
C=O OR CR OR 0.100 3 0.00
C=O OR CR HCMM 0.286 1 0.00
C=O OR CR HCMM -0.152 3 0.00
CR NC=O C=O O=C -0.160 1 0.00
CR NC=O C=O O=C 3.147 2 180.00
CR NC=O C=O O=C -0.073 3 0.00
CR CR CR C=O 0.033 1 0.00
CR CR CR C=O -0.078 2 180.00
CR CR CR C=O 0.071 3 0.00
CR CR CR HCMM 0.320 1 0.00
CR CR CR HCMM -0.315 2 180.00
CR CR CR HCMM 0.132 3 0.00
CR C=O OR HOCO -0.583 1 0.00
CR C=O OR HOCO 2.539 2 180.00
CR C=O OR HOCO -0.273 3 0.00
CR CR NC=O C=O -0.513 1 0.00
CR CR NC=O C=O 0.347 2 180.00
CR CR NC=O C=O 0.474 3 0.00
CR CR NC=O HNCO 0.276 1 0.00
CR CR NC=O HNCO -0.190 2 180.00
CR CR NC=O HNCO 0.163 3 0.00
CR C=O NC=O OR -0.517 1 0.00
CR C=O NC=O OR 4.396 2 180.00
CR C=O NC=O OR 0.732 3 0.00
CR C=O NC=O HNCO -0.147 1 0.00
CR C=O NC=O HNCO 2.902 2 180.00
CR C=O NC=O HNCO 0.671 3 0.00
C=O CB CB HCMM 1.000 2 180.00
C=O NC=O CR C=O 1.550 1 0.00
C=O NC=O CR C=O -1.264 2 180.00
C=O NC=O CR C=O 0.747 3 0.00
C=O NC=O CR HCMM -1.050 1 0.00
C=O NC=O CR HCMM 0.681 2 180.00
C=O NC=O CR HCMM 0.011 3 0.00
C=O CR NC=O HNCO 0.040 1 0.00
C=O CR NC=O HNCO 0.140 2 180.00
C=O CR NC=O HNCO 0.201 3 0.00
CR CB CB HCMM 3.500 2 180.00
C=O NC=O OR CR 0.600 1 0.00
C=O NC=O OR CR 0.250 2 180.00
C=O NC=O OR CR -0.500 3 0.00
CR OR C=O O=C 0.341 1 0.00
CR OR C=O O=C 3.592 2 180.00
CR OR C=O O=C -0.468 3 0.00
CR OR NC=O HNCO 0.600 1 0.00
CR OR NC=O HNCO 0.250 2 180.00
CR OR NC=O HNCO -0.500 3 0.00
OR CR CR HCMM -0.327 1 0.00
OR CR CR HCMM 0.536 2 180.00
OR CR CR HCMM 0.140 3 0.00
OR CR C=O OR 0.224 1 0.00
OR CR C=O OR 0.326 2 180.00
OR CR C=O OR 0.159 3 0.00
OR CR C=O O=C -0.198 1 0.00
OR CR C=O O=C 0.365 2 180.00
OR CR C=O O=C -0.070 3 0.00
OR C=O CR HCMM -0.312 2 180.00
OR C=O CR HCMM 0.165 3 0.00
OR CR CR OR 0.204 1 0.00
OR CR CR OR 0.699 2 180.00
OR CR CR OR 0.480 3 0.00
OR CR OR HOR 0.744 1 0.00
OR CR OR HOR -1.700 2 180.00
OR CR OR HOR -0.160 3 0.00
O=C C=O CR HCMM 0.330 1 0.00
O=C C=O CR HCMM -0.704 2 180.00
O=C C=O CR HCMM 0.154 3 0.00
O=C C=O NC=O HNCO 0.718 1 0.00
O=C C=O NC=O HNCO 2.487 2 180.00
O=C C=O NC=O HNCO -0.227 3 0.00
O=C C=O OR HOCO 0.831 1 0.00
O=C C=O OR HOCO 3.076 2 180.00
O=C C=O OR HOCO -0.029 3 0.00
O=C C=O NC=O OR 0.553 1 0.00
O=C C=O NC=O OR 4.316 2 180.00
O=C C=O NC=O OR -0.226 3 0.00
HCMM CR CR HCMM 0.142 1 0.00
HCMM CR CR HCMM -0.693 2 180.00
HCMM CR CR HCMM 0.157 3 0.00
HCMM CR OR HOR 0.298 1 0.00
HCMM CR OR HOR -0.138 2 180.00
HCMM CR OR HOR 0.173 3 0.00
HCMM CR NC=O HNCO -0.308 1 0.00
HCMM CR NC=O HNCO 0.137 3 0.00
HCMM CR NC=C HNCO -0.049 2 180.00
HCMM CR NC=C HNCO 0.102 3 0.00
HCMM CB CB HCMM 3.500 2 180.00
IMPROPER
CB CR NPYD CB 2.519 0 0.00
CB NPYD CB HCMM 3.310 0 0.00
CB CB NPYD N=C 2.519 0 0.00
CB CB NPYD C=O 2.519 0 0.00
C=O NC=O CB O=C 9.356 0 0.00
NC=O C=O C=O HNCO -2.159 0 0.00
CR NC=C CB HCMM 0.000 0 0.00
NC=C CB CR HNCO -0.432 0 0.00
CB CB NC=C CB 3.310 0 0.00
CB CB CB HCMM 1.079 0 0.00
CB C=O CB CB 1.943 0 0.00
C=O N=C NC=O NC=C 9.356 0 0.00
NC=O CR C=O HNCO -1.439 0 0.00
CR CR NC=O C=O 0.000 0 0.00
CR CR NC=O HCMM 0.000 0 0.00
CR CR CR HCMM 0.000 0 0.00
CR C=O CR HCMM 0.000 0 0.00
C=O NC=O CR O=C 9.284 0 0.00
C=O OR CR O=C 10.147 0 0.00
NC=O OR C=O HNCO -1.439 0 0.00
CR CR OR HCMM 0.000 0 0.00
CR OR CR OR 0.000 0 0.00
CR OR CR HCMM 0.000 0 0.00
C=O CR OR O=C 10.147 0 0.00
CR OR C=O CR 0.000 0 0.00
CR CR C=O HCMM 0.000 0 0.00
CR HCMM CR HCMM 0.000 0 0.00
NC=C HNCO C=O HNCO -0.504 0 0.00
NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch -
cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
NPYD 0.000000 -0.200000 1.850000
NC=O 0.000000 -0.200000 1.850000
N=C 0.000000 -0.200000 1.850000
CB 0.000000 -0.070000 1.992400
C=O 0.000000 -0.110000 2.000000
NC=C 0.000000 -0.200000 1.850000
CR 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000
OR 0.000000 -0.152100 1.770000
O=C 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000
HCMM 0.000000 -0.022000 1.320000
HOR 0.000000 -0.046000 0.224500
HNCO 0.000000 -0.046000 0.224500
HOCO 0.000000 -0.046000 0.224500