# Ligand structure changes after energy minimization using Steep descent algorithm **URL:** \ **Category:** User discussions\ **Created:** [August 23, 2022, 3:20pm UTC](https://gromacs.bioexcel.eu/t/ligand-structure-changes-after-energy-minimization-using-steep-descent-algorithm/4664 "2022-08-23T15:20:40Z")\ **Posts on this page:** 10\ **Page:** 1
**Author:** ![SavioC](https://avatars.discourse-cdn.com/v4/letter/s/eada6e/32.png) [@SavioC](https://gromacs.bioexcel.eu/u/SavioC)\ **Post date:** [August 23, 2022, 3:20pm UTC](https://gromacs.bioexcel.eu/t/ligand-structure-changes-after-energy-minimization-using-steep-descent-algorithm/4664/1 "2022-08-23T15:20:40Z")
GROMACS version: 2019 GROMACS modification: Yes/No Here post your question I did energy minimization of my ligand and the em.gro file contained a structure with same no of atoms but different bonds between the carbon atoms. The structure of 6,5-fused bicyclic moiety was completey different. What is the reason ---
**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:** [August 23, 2022, 4:00pm UTC](https://gromacs.bioexcel.eu/t/ligand-structure-changes-after-energy-minimization-using-steep-descent-algorithm/4664/2 "2022-08-23T16:00:31Z")
Please provide screenshots or coordinate files of the molecule. Note that bonds that you see in visualization software have no meaning; they are guessed by the software itself based on interatomic distances. Make sure you are not ignoring warnings from `grompp` about mismatched atom names, as these indicate incompatibility between the coordinates and topology that will lead to problems. ---
**Author:** ![SavioC](https://avatars.discourse-cdn.com/v4/letter/s/eada6e/32.png) [@SavioC](https://gromacs.bioexcel.eu/u/SavioC)\ **Post date:** [August 23, 2022, 4:09pm UTC](https://gromacs.bioexcel.eu/t/ligand-structure-changes-after-energy-minimization-using-steep-descent-algorithm/4664/3 "2022-08-23T16:09:40Z")
![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/9/97b3d046135f6d8a1354971f0f504b9fb44032cb.png) My initial structure ---
**Author:** ![SavioC](https://avatars.discourse-cdn.com/v4/letter/s/eada6e/32.png) [@SavioC](https://gromacs.bioexcel.eu/u/SavioC)\ **Post date:** [August 23, 2022, 4:12pm UTC](https://gromacs.bioexcel.eu/t/ligand-structure-changes-after-energy-minimization-using-steep-descent-algorithm/4664/4 "2022-08-23T16:12:08Z")
![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/5/5f892285330941dbf575331708f2b9102d7ec6b4.png) Final structure ---
**Author:** ![SavioC](https://avatars.discourse-cdn.com/v4/letter/s/eada6e/32.png) [@SavioC](https://gromacs.bioexcel.eu/u/SavioC)\ **Post date:** [August 23, 2022, 4:13pm UTC](https://gromacs.bioexcel.eu/t/ligand-structure-changes-after-energy-minimization-using-steep-descent-algorithm/4664/5 "2022-08-23T16:13:21Z")
Only after energy minimization i got such extra bonds in my ligand. I used Swissparam for generation of ligand topolgy. ---
**Author:** ![SavioC](https://avatars.discourse-cdn.com/v4/letter/s/eada6e/32.png) [@SavioC](https://gromacs.bioexcel.eu/u/SavioC)\ **Post date:** [August 23, 2022, 4:21pm UTC](https://gromacs.bioexcel.eu/t/ligand-structure-changes-after-energy-minimization-using-steep-descent-algorithm/4664/6 "2022-08-23T16:21:14Z")
[em.log](https://gromacs.bioexcel.eu/uploads/short-url/af6TxnTMzBTm7p22TXONLK4rrfZ.log) (879.4 KB) log file ---
**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:** [August 23, 2022, 5:28pm UTC](https://gromacs.bioexcel.eu/t/ligand-structure-changes-after-energy-minimization-using-steep-descent-algorithm/4664/7 "2022-08-23T17:28:25Z")
The `.log` file does not suggest anything particularly useful. Does `grompp` issue any notes or warnings? The collapse of the five-membered ring into a four-membered ring and the subsequent displacement of one N atom suggests something very wrong with the topology. ---
**Author:** ![SavioC](https://avatars.discourse-cdn.com/v4/letter/s/eada6e/32.png) [@SavioC](https://gromacs.bioexcel.eu/u/SavioC)\ **Post date:** [August 24, 2022, 6:52am UTC](https://gromacs.bioexcel.eu/t/ligand-structure-changes-after-energy-minimization-using-steep-descent-algorithm/4664/8 "2022-08-24T06:52:25Z")
Hi Professor. I have not noticed any warnings or notes in the grompp. I am attaching the str file for the ligand.mol2. - Toppar stream file generated by - CHARMM General Force Field (CGenFF) program version 2.5 - For use with CGenFF version 4.6 - read rtf card append - Topologies generated by - CHARMM General Force Field (CGenFF) program version 2.5 - 36 1 ! “penalty” is the highest penalty score of the associated parameters. ! Penalties lower than 10 indicate the analogy is fair; penalties between 10 ! and 50 mean some basic validation is recommended; penalties higher than ! 50 indicate poor analogy and mandate extensive validation/optimization. RESI 7L1F 0.000 ! param penalty= 288.500 ; charge penalty= 69.837 GROUP ! CHARGE CH\_PENALTY ATOM P1 PG0 1.476 ! 0.000 ATOM P2 PG0 1.495 ! 0.000 ATOM P3 PG0 1.456 ! 0.000 ATOM O1 OG3C51 -0.631 ! 16.554 ATOM O2 OG311 -0.650 ! 4.977 ATOM O3 OG311 -0.647 ! 0.040 ATOM O4 OG303 -0.636 ! 0.000 ATOM O5 OG304 -0.648 ! 0.000 ATOM O6 OG311 -0.606 ! 0.000 ATOM O7 OG2P1 -0.620 ! 0.000 ATOM O8 OG304 -0.582 ! 0.000 ATOM O9 OG311 -0.630 ! 0.000 ATOM O10 OG2P1 -0.617 ! 0.000 ATOM O11 OG311 -0.644 ! 0.000 ATOM O12 OG311 -0.644 ! 0.000 ATOM O13 OG2P1 -0.632 ! 0.000 ATOM N1 NG2RC0 -0.073 ! 69.837 ATOM N2 NG2R62 -0.475 ! 45.406 ATOM N3 NG2R62 -0.781 ! 28.183 ATOM N4 NG2S3 -0.764 ! 22.006 ATOM C1 CG3C50 0.430 ! 39.691 ATOM C2 CG3C51 0.038 ! 22.458 ATOM C3 CG3C51 0.100 ! 8.792 ATOM C4 CG3C51 0.172 ! 4.373 ATOM C5 CG2R57 0.303 ! 55.431 ATOM C6 CG321 -0.063 ! 0.304 ATOM C7 CG2R57 1.130 ! 48.352 ATOM C8 CG2R51 -0.308 ! 19.354 ATOM C9 CG2RC0 -0.145 ! 53.697 ATOM C10 CG2R51 -0.226 ! 20.406 ATOM C11 CG2R64 0.496 ! 38.049 ATOM C12 CG2R64 0.795 ! 28.027 ATOM N5 NG2R50 -0.692 ! 28.959 ATOM N6 NG2R50 -0.405 ! 10.964 ATOM N7 NG2R51 0.621 ! 19.128 ATOM N8 NG2R50 -0.831 ! 31.323 ATOM H1 HGP1 0.420 ! 0.040 ATOM H2 HGP1 0.420 ! 0.000 ATOM H3 HGP1 0.420 ! 0.000 ATOM H4 HGP1 0.420 ! 0.000 ATOM H5 HGP1 0.420 ! 0.000 ATOM H6 HGP1 0.420 ! 0.000 ATOM H7 HGP4 0.377 ! 0.000 ATOM H8 HGP4 0.377 ! 0.000 ATOM H9 HGA1 0.090 ! 0.723 ATOM H10 HGA1 0.090 ! 0.040 ATOM H11 HGA1 0.090 ! 0.040 ATOM H12 HGA2 0.090 ! 0.000 ATOM H13 HGA2 0.090 ! 0.000 ATOM H14 HGR51 0.188 ! 3.138 ATOM H15 HGR51 0.199 ! 0.376 ATOM H16 HGR62 0.081 ! 15.855 ATOM H17 HGP1 0.246 ! 0.827 BOND P1 O4 BOND P1 O5 BOND P1 O6 BOND P1 O7 BOND P2 O5 BOND P2 O8 BOND P2 O9 BOND P2 O10 BOND P3 O8 BOND P3 O11 BOND P3 O12 BOND P3 O13 BOND O1 C1 BOND O1 C4 BOND O2 C2 BOND O2 H1 BOND O3 C3 BOND O3 H2 BOND O4 C6 BOND O6 H3 BOND O9 H4 BOND O11 H5 BOND O12 H6 BOND N1 N2 BOND N1 C5 BOND N1 C9 BOND N2 C12 BOND N3 C11 BOND N3 C12 BOND N4 C11 BOND N4 H7 BOND N4 H8 BOND C1 C2 BOND C1 C5 BOND C1 C7 BOND C2 C3 BOND C2 H9 BOND C3 C4 BOND C3 H10 BOND C4 C6 BOND C4 H11 BOND C5 C8 BOND C6 H12 BOND C6 H13 BOND C7 N5 BOND C7 N8 BOND C8 C10 BOND C8 H14 BOND C9 C10 BOND C9 C11 BOND C10 H15 BOND C12 H16 BOND N5 N6 BOND N6 N7 BOND N7 N8 BOND N7 H17 IMPR N4 H8 H7 C11 IMPR C11 C9 N3 N4 END read param card flex append - Parameters generated by analogy by - CHARMM General Force Field (CGenFF) program version 2.5 - ! Penalties lower than 10 indicate the analogy is fair; penalties between 10 ! and 50 mean some basic validation is recommended; penalties higher than ! 50 indicate poor analogy and mandate extensive validation/optimization. BONDS CG2R57 CG3C50 350.00 1.5100 ! 7L1F , from CG2R51 CG3C50, penalty= 15 CG2R57 NG2R50 400.00 1.3800 ! 7L1F , from CG2R51 NG2R50, penalty= 15 CG2R57 NG2RC0 400.00 1.3710 ! 7L1F , from CG2R51 NG2RC0, penalty= 15 CG3C50 CG3C51 195.00 1.5180 ! 7L1F , from CG3C50 CG3C52, penalty= 4 CG3C50 OG3C51 350.00 1.4250 ! 7L1F , from CG3C51 OG3C51, penalty= 6 NG2R62 NG2RC0 420.00 1.3200 ! 7L1F , from NG2R62 NG2R62, penalty= 240 ANGLES CG2R51 CG2R57 CG3C50 115.00 109.00 ! 7L1F , from CG2R51 CG2R51 CG3C50, penalty= 15 CG2R51 CG2R57 NG2RC0 130.00 108.20 ! 7L1F , from CG2R51 CG2R51 NG2RC0, penalty= 15 CG3C50 CG2R57 NG2R50 170.00 112.00 ! 7L1F , from CG3C52 CG2R52 NG2R50, penalty= 21.2 CG3C50 CG2R57 NG2RC0 170.00 112.00 ! 7L1F , from CG3C52 CG2R52 NG2R50, penalty= 45.2 NG2R50 CG2R57 NG2R50 100.00 111.00 ! 7L1F , from NG2R50 CG2R53 NG2R50, penalty= 43 CG2R51 CG2RC0 CG2R64 130.00 132.00 ! 7L1F , from CG2R51 CG2RC0 CG2R63, penalty= 0.5 CG2R64 CG2RC0 NG2RC0 80.00 118.80 ! 7L1F , from CG2R61 CG2RC0 NG2RC0, penalty= 3 CG2R57 CG3C50 CG2R57 45.00 103.00 ! 7L1F , from CG2R53 CG3C50 CG2RC0, penalty= 10 CG2R57 CG3C50 CG3C51 112.00 102.70 ! 7L1F , from CG2R51 CG3C51 CG3C51, penalty= 6.5 CG2R57 CG3C50 OG3C51 75.00 102.40 ! 7L1F , from CG2R51 CG3C52 OG3C51, penalty= 10.5 CG3C51 CG3C50 OG3C51 45.00 111.10 ! 7L1F , from CG3C51 CG3C51 OG3C51, penalty= 6 CG3C50 CG3C51 CG3C51 58.00 109.50 11.16 2.56100 ! 7L1F , from CG3C51 CG3C51 CG3C51, penalty= 0.8 CG3C50 CG3C51 OG311 75.70 110.10 ! 7L1F , from CG3C51 CG3C51 OG311, penalty= 0.8 CG3C50 CG3C51 HGA1 35.00 111.40 22.53 2.17900 ! 7L1F , from CG3C51 CG3C51 HGA1, penalty= 0.8 CG2R57 NG2R50 NG2R50 110.00 106.80 ! 7L1F , from CG2R51 NG2R50 NG2R50, penalty= 0.5 CG2R57 NG2R50 NG2R51 160.00 103.50 ! 7L1F , from CG2R52 NG2R50 NG2R51, penalty= 2 CG2R64 NG2R62 NG2RC0 65.00 121.00 ! 7L1F , from CG2R64 NG2R62 NG2R62, penalty= 27 CG2R57 NG2RC0 CG2RC0 100.00 109.70 ! 7L1F , from CG2R51 NG2RC0 CG2RC0, penalty= 0.5 CG2R57 NG2RC0 NG2R62 15.00 130.50 ! 7L1F , from CG2R51 NG2RC0 CG2R61, penalty= 45.5 CG2RC0 NG2RC0 NG2R62 15.00 119.80 ! 7L1F , from CG2R61 NG2RC0 CG2RC0, penalty= 45 CG3C50 OG3C51 CG3C51 95.00 111.00 ! 7L1F , from CG3C51 OG3C51 CG3C51, penalty= 0.8 DIHEDRALS CG2R57 CG2R51 CG2R51 CG2RC0 2.0000 2 180.00 ! 7L1F , from CG2R51 CG2R51 CG2R51 CG2RC0, penalty= 0.5 CG2R57 CG2R51 CG2R51 HGR51 1.5000 2 180.00 ! 7L1F , from CG2R57 CG2R51 CG2R51 HGR52, penalty= 0.5 CG2R51 CG2R51 CG2R57 CG3C50 4.0000 2 180.00 ! 7L1F , from CG2R51 CG2R51 CG2R51 CG3C52, penalty= 16.2 CG2R51 CG2R51 CG2R57 NG2RC0 16.0000 2 180.00 ! 7L1F , from CG2R51 CG2R51 CG2R51 NG2RC0, penalty= 15 HGR51 CG2R51 CG2R57 CG3C50 2.9000 2 180.00 ! 7L1F , from CG3C50 CG2R51 CG2R51 HGR51, penalty= 15 HGR51 CG2R51 CG2R57 NG2RC0 3.7000 2 180.00 ! 7L1F , from NG2RC0 CG2R51 CG2R51 HGR51, penalty= 15 CG2R51 CG2R51 CG2RC0 CG2R64 3.0000 2 180.00 ! 7L1F , from CG2R51 CG2R51 CG2RC0 CG2R63, penalty= 0.5 HGR51 CG2R51 CG2RC0 CG2R64 2.8000 2 180.00 ! 7L1F , from HGR51 CG2R51 CG2RC0 CG2R63, penalty= 0.5 CG2R51 CG2R57 CG3C50 CG2R57 2.0500 3 180.00 ! 7L1F , from CG2R51 CG2R51 CG3C52 CG2R51, penalty= 25.5 CG2R51 CG2R57 CG3C50 CG3C51 0.3500 3 180.00 ! 7L1F , from CG2R51 CG2R51 CG3C51 CG3C51, penalty= 21 CG2R51 CG2R57 CG3C50 OG3C51 0.2800 1 180.00 ! 7L1F , from CG2R51 CG2R51 CG3C52 OG3C51, penalty= 25 CG2R51 CG2R57 CG3C50 OG3C51 0.9800 2 180.00 ! 7L1F , from CG2R51 CG2R51 CG3C52 OG3C51, penalty= 25 CG2R51 CG2R57 CG3C50 OG3C51 1.7500 3 180.00 ! 7L1F , from CG2R51 CG2R51 CG3C52 OG3C51, penalty= 25 NG2R50 CG2R57 CG3C50 CG2R57 3.5000 3 180.00 ! 7L1F , from NG2R50 CG2R52 CG3C52 CG2R51, penalty= 30.5 NG2R50 CG2R57 CG3C50 CG3C51 2.8000 3 180.00 ! 7L1F , from NG2R50 CG2R52 CG3C52 CG3C52, penalty= 30.4 NG2R50 CG2R57 CG3C50 OG3C51 0.2800 1 180.00 ! 7L1F , from CG2R51 CG2R51 CG3C52 OG3C51, penalty= 71.5 NG2R50 CG2R57 CG3C50 OG3C51 0.9800 2 180.00 ! 7L1F , from CG2R51 CG2R51 CG3C52 OG3C51, penalty= 71.5 NG2R50 CG2R57 CG3C50 OG3C51 1.7500 3 180.00 ! 7L1F , from CG2R51 CG2R51 CG3C52 OG3C51, penalty= 71.5 NG2RC0 CG2R57 CG3C50 CG2R57 3.5000 3 180.00 ! 7L1F , from NG2R50 CG2R52 CG3C52 CG2R51, penalty= 54.5 NG2RC0 CG2R57 CG3C50 CG3C51 2.8000 3 180.00 ! 7L1F , from NG2R50 CG2R52 CG3C52 CG3C52, penalty= 54.4 NG2RC0 CG2R57 CG3C50 OG3C51 0.2800 1 180.00 ! 7L1F , from CG2R51 CG2R51 CG3C52 OG3C51, penalty= 73.5 NG2RC0 CG2R57 CG3C50 OG3C51 0.9800 2 180.00 ! 7L1F , from CG2R51 CG2R51 CG3C52 OG3C51, penalty= 73.5 NG2RC0 CG2R57 CG3C50 OG3C51 1.7500 3 180.00 ! 7L1F , from CG2R51 CG2R51 CG3C52 OG3C51, penalty= 73.5 CG3C50 CG2R57 NG2R50 NG2R50 6.5000 2 180.00 ! 7L1F , from CG3C52 CG2R52 NG2R50 CG2R51, penalty= 67.7 CG3C50 CG2R57 NG2R50 NG2R51 3.8000 2 180.00 ! 7L1F , from CG321 CG2R52 NG2R50 NG2R51, penalty= 50 NG2R50 CG2R57 NG2R50 NG2R50 12.5512 2 180.00 ! 7L1F , from NG2R50 CG2R53 NG2R50 NG2R50, penalty= 43 NG2R50 CG2R57 NG2R50 NG2R51 12.0000 2 180.00 ! 7L1F , from NG2R50 CG2R53 NG2R50 NG2R51, penalty= 43 CG2R51 CG2R57 NG2RC0 CG2RC0 9.0000 2 180.00 ! 7L1F , from CG2R51 CG2R51 NG2RC0 CG2RC0, penalty= 15 CG2R51 CG2R57 NG2RC0 NG2R62 3.0000 2 180.00 ! 7L1F , from CG2R51 CG2R51 NG2RC0 CG2R61, penalty= 60 CG3C50 CG2R57 NG2RC0 CG2RC0 0.7000 2 180.00 ! 7L1F , from CG321 CG2R51 NG2RC0 CG2RC0, penalty= 45 CG3C50 CG2R57 NG2RC0 NG2R62 0.7000 2 180.00 ! 7L1F , from CG321 CG2R51 NG2RC0 CG2R61, penalty= 90 NG2R62 CG2R64 CG2RC0 CG2R51 2.2000 2 180.00 ! 7L1F , from NG2R62 CG2R61 CG2RC0 CG2R51, penalty= 15 NG2R62 CG2R64 CG2RC0 NG2RC0 0.0000 2 180.00 ! 7L1F , from NG2R62 CG2R61 CG2RC0 NG2R51, penalty= 38 NG2S3 CG2R64 CG2RC0 CG2R51 1.1583 2 180.00 ! 7L1F , from NG2S3 CG2R61 CG2RC0 CG2R51, penalty= 15 NG2S3 CG2R64 CG2RC0 NG2RC0 0.0000 2 180.00 ! 7L1F , from NG2S3 CG2R64 CG2RC0 NG2R50, penalty= 44 NG2R62 CG2R64 NG2R62 NG2RC0 0.5000 2 180.00 ! 7L1F , from NG2R62 CG2R64 NG2R62 NG2R62, penalty= 27 HGR62 CG2R64 NG2R62 NG2RC0 6.0000 2 180.00 ! 7L1F , from HGR62 CG2R64 NG2R62 NG2R62, penalty= 27 CG2R51 CG2RC0 NG2RC0 CG2R57 8.0000 2 180.00 ! 7L1F , from CG2R51 CG2RC0 NG2RC0 CG2R51, penalty= 0.5 CG2R51 CG2RC0 NG2RC0 NG2R62 1.0000 2 180.00 ! 7L1F , from CG2R51 CG2RC0 NG2RC0 CG2R61, penalty= 45 CG2R64 CG2RC0 NG2RC0 CG2R57 1.0000 2 180.00 ! 7L1F , from CG2R61 CG2RC0 NG2RC0 CG2R51, penalty= 3.5 CG2R64 CG2RC0 NG2RC0 NG2R62 0.8000 2 180.00 ! 7L1F , from CG2R61 CG2RC0 NG2RC0 CG2R61, penalty= 48 CG2R57 CG3C50 CG3C51 CG3C51 0.3400 3 180.00 ! 7L1F , from CG2R51 CG3C51 CG3C51 CG3C51, penalty= 6.5 CG2R57 CG3C50 CG3C51 OG311 0.1400 3 0.00 ! 7L1F , from CG2R51 CG3C51 CG3C51 OG311, penalty= 6.5 CG2R57 CG3C50 CG3C51 HGA1 0.1900 3 0.00 ! 7L1F , from CG2R51 CG3C51 CG3C51 HGA1, penalty= 6.5 OG3C51 CG3C50 CG3C51 CG3C51 0.0000 3 0.00 ! 7L1F , from CG3C51 CG3C51 CG3C51 OG3C51, penalty= 6 OG3C51 CG3C50 CG3C51 OG311 0.2000 3 0.00 ! 7L1F , from OG311 CG3C51 CG3C51 OG3C51, penalty= 6 OG3C51 CG3C50 CG3C51 OG311 0.6000 4 180.00 ! 7L1F , from OG311 CG3C51 CG3C51 OG3C51, penalty= 6 OG3C51 CG3C50 CG3C51 OG311 0.3000 5 0.00 ! 7L1F , from OG311 CG3C51 CG3C51 OG3C51, penalty= 6 OG3C51 CG3C50 CG3C51 OG311 0.5000 6 0.00 ! 7L1F , from OG311 CG3C51 CG3C51 OG3C51, penalty= 6 OG3C51 CG3C50 CG3C51 HGA1 0.1900 3 0.00 ! 7L1F , from OG3C51 CG3C51 CG3C51 HGA1, penalty= 6 CG2R57 CG3C50 OG3C51 CG3C51 0.0000 3 0.00 ! 7L1F , from NG2R51 CG3C51 OG3C51 CG3C51, penalty= 58 CG3C51 CG3C50 OG3C51 CG3C51 0.5000 3 0.00 ! 7L1F , from CG3C51 CG3C51 OG3C51 CG3C51, penalty= 6 CG3C50 CG3C51 CG3C51 CG3C51 0.4100 3 180.00 ! 7L1F , from CG3C51 CG3C51 CG3C51 CG3C51, penalty= 0.8 CG3C50 CG3C51 CG3C51 OG311 0.2000 3 0.00 ! 7L1F , from CG3C51 CG3C51 CG3C51 OG311, penalty= 0.8 CG3C50 CG3C51 CG3C51 HGA1 0.1900 3 0.00 ! 7L1F , from CG3C51 CG3C51 CG3C51 HGA1, penalty= 0.8 CG3C50 CG3C51 OG311 HGP1 0.2900 1 0.00 ! 7L1F , from CG3C51 CG3C51 OG311 HGP1, penalty= 0.8 CG3C50 CG3C51 OG311 HGP1 0.6200 2 0.00 ! 7L1F , from CG3C51 CG3C51 OG311 HGP1, penalty= 0.8 CG3C50 CG3C51 OG311 HGP1 0.0500 3 0.00 ! 7L1F , from CG3C51 CG3C51 OG311 HGP1, penalty= 0.8 CG321 CG3C51 OG3C51 CG3C50 0.3000 3 0.00 ! 7L1F , from CG321 CG3C51 OG3C51 CG3C51, penalty= 0.8 CG3C51 CG3C51 OG3C51 CG3C50 0.5000 3 0.00 ! 7L1F , from CG3C51 CG3C51 OG3C51 CG3C51, penalty= 0.8 HGA1 CG3C51 OG3C51 CG3C50 0.3000 3 0.00 ! 7L1F , from HGA1 CG3C51 OG3C51 CG3C51, penalty= 0.8 CG2R57 NG2R50 NG2R50 NG2R51 14.0000 2 180.00 ! 7L1F , from CG2R51 NG2R50 NG2R50 NG2R51, penalty= 0.5 CG2R57 NG2R50 NG2R51 NG2R50 9.5000 2 180.00 ! 7L1F , from CG2R52 NG2R50 NG2R51 NG2R50, penalty= 2 CG2R57 NG2R50 NG2R51 HGP1 1.4000 2 180.00 ! 7L1F , from CG2R52 NG2R50 NG2R51 HGP1, penalty= 2 CG2R64 NG2R62 NG2RC0 CG2R57 0.5000 2 180.00 ! 7L1F , from CG2R61 NG2R62 NG2R62 CG2R64, penalty= 288.5 CG2R64 NG2R62 NG2RC0 CG2RC0 0.5000 2 180.00 ! 7L1F , from CG2R61 NG2R62 NG2R62 CG2R64, penalty= 281.5 IMPROPERS END RETURN ---
**Author:** ![ggsmith123](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/ggsmith123/32/520_2.png) [@ggsmith123](https://gromacs.bioexcel.eu/u/ggsmith123)\ **Post date:** [August 30, 2022, 4:21pm UTC](https://gromacs.bioexcel.eu/t/ligand-structure-changes-after-energy-minimization-using-steep-descent-algorithm/4664/9 "2022-08-30T16:21:36Z")
Hi Savio, I don’t know that I can add a huge amount to what Justin said; he knows way more than me, but as somebody who has worked on custom force fields and topologies, I can give a couple pointers. First, it’s really clear that there’s something deeply wrong in your topology. I would recommend digging into the \*.top file that you’re feeding gromacs and look particularly at the centers being affected by the distortion to make certain they’ve been properly assigned. Second, I would be wary of just using an automatically generated \*.top file. The images of the molecules you’ve provided above suggest something like a DNA purine ring system, but there is a questionable assignment that has nitrogen-nitrogen bonding in the ring. Purines don’t have internal azo-linkages and an automated program that is optimized to DNA or protein is probably going to choke trying to assign topology to something like this. I seriously doubt even OPLS would have the appropriate types for this kind of structure; it’s just too strange. If that azo-linkage inside the rings is really what you intend, you probably need to determine your own types. (I’m still trying to wrap my head around the liganding; it seems like it would need a full positive charge on the tertiary amine, making it quaternary in order to deal with the neighboring nitrogen, which is only secondary… is that really what you intend?). Third, if that bicyclic compound in the picture is actually supposed to be adenine, that’s probably a big part of your problem; that’s not an adenine structure and it won’t be assigned like an adenine. Good luck! Greg ---
**Author:** ![SavioC](https://avatars.discourse-cdn.com/v4/letter/s/eada6e/32.png) [@SavioC](https://gromacs.bioexcel.eu/u/SavioC)\ **Post date:** [August 31, 2022, 8:02am UTC](https://gromacs.bioexcel.eu/t/ligand-structure-changes-after-energy-minimization-using-steep-descent-algorithm/4664/10 "2022-08-31T08:02:33Z")
Hi Greg, The molecule is an analog of Remdesivir which contains a pyrrolo[2,1-f][1,2,4]triazin-4-amine as nucleobase, and thus has that N-N bond you mentioned. How can I make generate parameters for this molecule???