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