Swissparm prm file

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:


  • Built parameters for REC.mol2
  • by user vzoete Mon Feb 1 21:26:10 UTC 2021

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

Your .prm file is formatted for CHARMM. It can’t be used in GROMACS without format and unit conversion.

how compatible this prm file for gromacs?

It’s not. Like I said, you’ll have to convert the format and units.

Thank you for your answer. How and by what tool should I do this?

Is cgenff2gromacs.py good for this?

Do you even need this file? The topologies (.itp) that SwissParam writes have all the parameters explicitly present. The .prm file should only be needed by CHARMM.

Do you mean that if we use the swissparm output itp file, we no longer need to include the prm file?

Because I get an error when working with cgenff and I do not know how to fix it.

They have instructions on their website for how to use their files: SwissParam - Topology and parameters for small organic molecules

The CGenFF conversion script is designed for use with the CGenFF web server, not SwissParam.

thanks Dr Justin A. Lemku