# Ligand parameterisation for CHARMM FF with CP2K **URL:** \ **Category:** User discussions\ **Tags:** qm-mm\ **Created:** [March 29, 2022, 2:48pm UTC](https://gromacs.bioexcel.eu/t/ligand-parameterisation-for-charmm-ff-with-cp2k/3919 "2022-03-29T14:48:22Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![Kash9](https://avatars.discourse-cdn.com/v4/letter/k/df788c/32.png) [@Kash9](https://gromacs.bioexcel.eu/u/Kash9)\ **Post date:** [March 29, 2022, 2:48pm UTC](https://gromacs.bioexcel.eu/t/ligand-parameterisation-for-charmm-ff-with-cp2k/3919/1 "2022-03-29T14:48:22Z")
GROMACS version: GROMACS modification: Yes/No Hi all, I have obtained an str file for a pyridoxamine 5’-phosphate (PMP) cofactor. From the str file, I can see that there are some high penalty values for dihedral and charges. Is it possible to use the CP2K with gromacs to fix those penalty values or do I have to turn to standalone tools like FFParam. I’ve pasted the str output below: - Toppar stream file generated by - CHARMM General Force Field (CGenFF) program version 2.5 - For use with CGenFF version 4.5 - 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 PMP 0.000 ! param penalty= 73.000 ; charge penalty= 42.325 GROUP ! CHARGE CH\_PENALTY ATOM P1 PG0 1.490 ! 2.500 ATOM O2 OG303 -0.622 ! 10.338 ATOM O3 OG311 -0.527 ! 0.511 ATOM O4 OG311 -0.622 ! 0.000 ATOM O5 OG311 -0.622 ! 0.000 ATOM O6 OG2P1 -0.620 ! 0.000 ATOM N7 NG2R60 -0.624 ! 42.325 ATOM N8 NG321 -0.814 ! 6.058 ATOM C9 CG2R61 0.010 ! 8.235 ATOM C10 CG2R61 -0.011 ! 6.583 ATOM C11 CG2R61 0.097 ! 0.813 ATOM C12 CG321 -0.022 ! 7.198 ATOM C13 CG321 -0.060 ! 5.909 ATOM C14 CG2R61 0.392 ! 36.130 ATOM C15 CG2R61 0.173 ! 6.478 ATOM C16 CG331 -0.309 ! 37.536 ATOM H17 HGA2 0.090 ! 0.000 ATOM H18 HGA2 0.090 ! 0.000 ATOM H19 HGA2 0.090 ! 0.000 ATOM H20 HGA2 0.090 ! 0.000 ATOM H21 HGR62 0.120 ! 0.000 ATOM H22 HGA3 0.090 ! 2.100 ATOM H23 HGA3 0.090 ! 2.100 ATOM H24 HGA3 0.090 ! 2.100 ATOM H25 HGPAM2 0.342 ! 4.364 ATOM H26 HGPAM2 0.342 ! 4.364 ATOM H27 HGP1 0.419 ! 0.000 ATOM H28 HGP1 0.419 ! 0.000 ATOM H29 HGP1 0.419 ! 0.000 BOND P1 O2 BOND P1 O4 BOND P1 O5 BOND P1 O6 BOND O2 C12 BOND O3 C11 BOND O3 H27 BOND O4 H28 BOND O5 H29 BOND N7 C14 BOND N7 C15 BOND N8 C13 BOND N8 H25 BOND N8 H26 BOND C9 C10 BOND C9 C11 BOND C9 C13 BOND C10 C12 BOND C10 C15 BOND C11 C14 BOND C12 H17 BOND C12 H18 BOND C13 H19 BOND C13 H20 BOND C14 C16 BOND C15 H21 BOND C16 H22 BOND C16 H23 BOND C16 H24 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 ANGLES CG2R61 CG321 NG321 73.00 109.00 ! PMP , from CG2R61 CG321 NG311, penalty= 1.2 CG2R61 CG321 OG303 75.70 110.10 ! PMP , from CG2R61 CG321 OG302, penalty= 2.5 DIHEDRALS CG321 CG2R61 CG2R61 CG321 2.4000 2 180.00 ! PMP , from CG331 CG2R61 CG2R61 CG331, penalty= 1.8 CG321 CG2R61 CG2R61 OG311 2.4000 2 180.00 ! PMP , from CG311 CG2R61 CG2R61 OG311, penalty= 0.6 CG2R61 CG2R61 CG321 NG321 1.0000 2 180.00 ! PMP , from CG2R61 CG2R61 CG321 NG311, penalty= 1.2 CG2R61 CG2R61 CG321 OG303 0.0000 2 0.00 ! PMP , from CG2R61 CG2R61 CG321 OG302, penalty= 2.5 CG2R61 CG321 NG321 HGPAM2 0.3000 3 0.00 ! PMP , from CG2R62 CG321 NG321 HGPAM2, penalty= 1.5 CG2R61 CG321 OG303 PG0 0.6000 1 180.00 ! PMP , from CG321 CG321 OG303 PG1, penalty= 73 CG2R61 CG321 OG303 PG0 0.6500 2 0.00 ! PMP , from CG321 CG321 OG303 PG1, penalty= 73 CG2R61 CG321 OG303 PG0 0.0500 3 0.00 ! PMP , from CG321 CG321 OG303 PG1, penalty= 73 IMPROPERS END RETURN Any guidance would be much appreciated. Thank you, Akash ---
**Author:** ![dmorozov](https://avatars.discourse-cdn.com/v4/letter/d/dec6dc/32.png) [@dmorozov](https://gromacs.bioexcel.eu/u/dmorozov)\ **Post date:** [April 5, 2022, 1:46pm UTC](https://gromacs.bioexcel.eu/t/ligand-parameterisation-for-charmm-ff-with-cp2k/3919/2 "2022-04-05T13:46:49Z")
Sorry for the late reply, Seems like CGenFF could not generate good parameters for your ligand. I think for that case you would need to follow standard CHARMM parametrization protocol. Don’t think that CP2K or GROMACS/CP2K could help you with that.