# Swissparm prm file **URL:** \ **Category:** User discussions\ **Created:** [February 8, 2021, 5:27pm UTC](https://gromacs.bioexcel.eu/t/swissparm-prm-file/1556 "2021-02-08T17:27:49Z")\ **Posts on this page:** 12\ **Page:** 1
**Author:** ![biotech70](https://avatars.discourse-cdn.com/v4/letter/b/a4c791/32.png) [@biotech70](https://gromacs.bioexcel.eu/u/biotech70)\ **Post date:** [February 8, 2021, 5:27pm UTC](https://gromacs.bioexcel.eu/t/swissparm-prm-file/1556/1 "2021-02-08T17:27:49Z")
GROMACS version: 2021 GROMACS modification: Yes/No Here post your question 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 ![topol](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/6b9da6372729ae72567ac302b9e274aa01f6313d.png) ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [February 8, 2021, 6:07pm UTC](https://gromacs.bioexcel.eu/t/swissparm-prm-file/1556/2 "2021-02-08T18:07:37Z")
Your `.prm` file is formatted for CHARMM. It can’t be used in GROMACS without format and unit conversion. ---
**Author:** ![biotech70](https://avatars.discourse-cdn.com/v4/letter/b/a4c791/32.png) [@biotech70](https://gromacs.bioexcel.eu/u/biotech70)\ **Post date:** [February 8, 2021, 8:43pm UTC](https://gromacs.bioexcel.eu/t/swissparm-prm-file/1556/3 "2021-02-08T20:43:24Z")
how compatible this prm file for gromacs? ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [February 8, 2021, 8:56pm UTC](https://gromacs.bioexcel.eu/t/swissparm-prm-file/1556/4 "2021-02-08T20:56:19Z")
It’s not. Like I said, you’ll have to convert the format and units. ---
**Author:** ![biotech70](https://avatars.discourse-cdn.com/v4/letter/b/a4c791/32.png) [@biotech70](https://gromacs.bioexcel.eu/u/biotech70)\ **Post date:** [February 8, 2021, 9:11pm UTC](https://gromacs.bioexcel.eu/t/swissparm-prm-file/1556/5 "2021-02-08T21:11:03Z")
Thank you for your answer. How and by what tool should I do this? ---
**Author:** ![biotech70](https://avatars.discourse-cdn.com/v4/letter/b/a4c791/32.png) [@biotech70](https://gromacs.bioexcel.eu/u/biotech70)\ **Post date:** [February 8, 2021, 9:21pm UTC](https://gromacs.bioexcel.eu/t/swissparm-prm-file/1556/6 "2021-02-08T21:21:54Z")
Is cgenff2gromacs.py good for this? ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [February 8, 2021, 9:27pm UTC](https://gromacs.bioexcel.eu/t/swissparm-prm-file/1556/7 "2021-02-08T21:27:03Z")
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. ---
**Author:** ![biotech70](https://avatars.discourse-cdn.com/v4/letter/b/a4c791/32.png) [@biotech70](https://gromacs.bioexcel.eu/u/biotech70)\ **Post date:** [February 8, 2021, 9:44pm UTC](https://gromacs.bioexcel.eu/t/swissparm-prm-file/1556/8 "2021-02-08T21:44:28Z")
Do you mean that if we use the swissparm output itp file, we no longer need to include the prm file? ---
**Author:** ![biotech70](https://avatars.discourse-cdn.com/v4/letter/b/a4c791/32.png) [@biotech70](https://gromacs.bioexcel.eu/u/biotech70)\ **Post date:** [February 8, 2021, 9:47pm UTC](https://gromacs.bioexcel.eu/t/swissparm-prm-file/1556/9 "2021-02-08T21:47:46Z")
Because I get an error when working with cgenff and I do not know how to fix it. ![error](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/d2da3c4d2f63d5a331ac92eda11c2921d210a3ef.png) ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [February 9, 2021, 1:36pm UTC](https://gromacs.bioexcel.eu/t/swissparm-prm-file/1556/10 "2021-02-09T13:36:40Z")
> [@biotech70](#): > > Do you mean that if we use the swissparm output itp file, we no longer need to include the prm file? They have instructions on their website for how to use their files: [https://www.swissparam.ch/SwissParam\_gromacs\_tutorial.html](https://www.swissparam.ch/SwissParam_gromacs_tutorial.html) > [@biotech70](#): > > Because I get an error when working with cgenff and I do not know how to fix it. The CGenFF conversion script is designed for use with the CGenFF web server, not SwissParam. ---
**Author:** ![biotech70](https://avatars.discourse-cdn.com/v4/letter/b/a4c791/32.png) [@biotech70](https://gromacs.bioexcel.eu/u/biotech70)\ **Post date:** [February 9, 2021, 3:58pm UTC](https://gromacs.bioexcel.eu/t/swissparm-prm-file/1556/11 "2021-02-09T15:58:23Z")
thanks Dr Justin A. Lemku ---
**Author:** ![vardhan](https://avatars.discourse-cdn.com/v4/letter/v/ebca7d/32.png) [@vardhan](https://gromacs.bioexcel.eu/u/vardhan)\ **Post date:** [January 22, 2025, 8:52am UTC](https://gromacs.bioexcel.eu/t/swissparm-prm-file/1556/12 "2025-01-22T08:52:28Z")
Hi Justin. I used Swiss Param to build the topology for a molecule (Triethyl Citrate). I did all the conversions and built a GROMACS compatible itp file. But, for a particular dihedral type it gave me five different values (for K, n, and angle). I choose the one with low energy (plot of angle vs potential) and low periodicity. Is this ok or should I use any other way to choose the parameters ? Thank you, Please