GROMACS version: 2020.1-Ubuntu-2020.1-1
GROMACS modification: Yes/No
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i have been trying to generate the ligand topology using cgenff server but it gives errors can anyone please suggest me how to do parametrization. i have also used charmmgui server it also gives me error when i tried to do simulation using the output files i got from such server
i have also attached the file.
- 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 LIG 0.000 ! param penalty= 200.000 ; charge penalty= 53.785
GROUP ! CHARGE CH_PENALTY
ATOM C1 CG331 -0.277 ! 3.203
ATOM C2 CG311 0.145 ! 5.310
ATOM H1 HGA1 0.090 ! 0.150
ATOM O1 OG311 -0.646 ! 1.897
ATOM C3 CG311 0.196 ! 20.057
ATOM H2 HGA1 0.090 ! 0.550
ATOM O2 OG303 -0.178 ! 24.558
ATOM S SG3O2 0.049 ! 53.785! typer WARNING: sulfuric or sulfonic acid not explicitly supported
ATOM O3 OG2P1 -0.203 ! 4.976
ATOM O4 OG2P1 -0.203 ! 4.976
ATOM O5 OG311 -0.091 ! 52.659
ATOM C4 CG311 0.110 ! 5.009
ATOM H3 HGA1 0.090 ! 0.157
ATOM O6 OG301 -0.392 ! 0.891
ATOM C5 CG321 0.010 ! 0.952
ATOM C6 CG311 0.143 ! 0.919
ATOM H4 HGA1 0.090 ! 0.025
ATOM O7 OG311 -0.645 ! 0.474
ATOM C7 CG311 0.115 ! 0.348
ATOM H5 HGA1 0.090 ! 0.000
ATOM O8 OG311 -0.646 ! 0.000
ATOM C8 CG311 0.142 ! 0.000
ATOM H6 HGA1 0.090 ! 0.000
ATOM O9 OG311 -0.644 ! 0.000
ATOM C9 CG321 0.057 ! 0.000
ATOM O10 OG311 -0.645 ! 0.000
ATOM C10 CG311 0.266 ! 17.001
ATOM H7 HGA1 0.090 ! 0.000
ATOM O11 OG311 -0.623 ! 16.594
ATOM C11 CG2O4 0.195 ! 3.235
ATOM O12 OG2D1 -0.400 ! 0.275
ATOM H8 HGA3 0.090 ! 0.000
ATOM H9 HGA3 0.090 ! 0.000
ATOM H10 HGA3 0.090 ! 0.000
ATOM H11 HGP1 0.419 ! 0.000
ATOM H12 HGP1 0.351 ! 11.101
ATOM H13 HGA2 0.090 ! 0.030
ATOM H14 HGA2 0.090 ! 0.030
ATOM H15 HGP1 0.419 ! 0.000
ATOM H16 HGP1 0.419 ! 0.000
ATOM H17 HGP1 0.419 ! 0.000
ATOM H18 HGA2 0.090 ! 0.000
ATOM H19 HGA2 0.090 ! 0.000
ATOM H20 HGP1 0.419 ! 0.000
ATOM H21 HGP1 0.369 ! 0.300
ATOM H22 HGR52 0.090 ! 2.280
BOND C1 C2
BOND C1 H8
BOND C1 H9
BOND C1 H10
BOND C2 H1
BOND C2 O1
BOND C2 C3
BOND O1 H11
BOND C3 H2
BOND C3 O2
BOND C3 C4
BOND O2 S
BOND S O3
BOND S O4
BOND S O5
BOND O5 H12
BOND C4 H3
BOND C4 O6
BOND C4 C10
BOND O6 C5
BOND C5 C6
BOND C5 H13
BOND C5 H14
BOND C6 H4
BOND C6 O7
BOND C6 C7
BOND O7 H15
BOND C7 H5
BOND C7 O8
BOND C7 C8
BOND O8 H16
BOND C8 H6
BOND C8 O9
BOND C8 C9
BOND O9 H17
BOND C9 O10
BOND C9 H18
BOND C9 H19
BOND O10 H20
BOND C10 H7
BOND C10 O11
BOND C10 C11
BOND O11 H21
BOND C11 O12
BOND C11 H22
IMPR C11 C10 O12 H22
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
OG311 SG3O2 235.00 1.6000 ! LIG , from OG303 SG3O2, penalty= 140
ANGLES
CG2O4 CG311 OG311 112.00 111.00 ! LIG , from CG2O5 CG311 OG311, penalty= 0.5
CG311 CG311 OG303 115.00 109.70 ! LIG , from CG331 CG311 OG303, penalty= 1.5
CG311 CG321 OG301 75.70 110.10 ! LIG , from CG311 CG321 OG302, penalty= 0.5
CG311 OG301 CG321 95.00 109.70 ! LIG , from CG321 OG301 CG321, penalty= 0.6
CG311 OG303 SG3O2 48.00 113.00 ! LIG , from CG331 OG303 SG3O2, penalty= 1.5
SG3O2 OG311 HGP1 30.00 115.00 40.00 2.35000 ! LIG , from PG1 OG311 HGP1, penalty= 16
OG2P1 SG3O2 OG311 90.00 109.00 ! LIG , from OG2P1 SG3O2 OG303, penalty= 6.5
OG303 SG3O2 OG311 100.00 102.00 ! LIG , from NG321 SG3O2 OG303, penalty= 34.2
DIHEDRALS
OG2D1 CG2O4 CG311 OG311 0.0000 2 0.00 ! LIG , from OG2D3 CG2O5 CG311 OG311, penalty= 10.5
HGR52 CG2O4 CG311 OG311 0.0000 3 180.00 ! LIG , from HGR52 CG2O4 CG311 CG311, penalty= 45.6
CG2O4 CG311 CG311 CG311 0.2000 3 0.00 ! LIG , from CG2O4 CG311 CG311 CG331, penalty= 1.5
CG311 CG311 CG311 CG311 0.5000 4 180.00 ! LIG , from CG311 CG311 CG311 CG321, penalty= 0.6
CG311 CG311 CG311 OG301 0.1600 1 180.00 ! LIG , from OG301 CG311 CG321 CG321, penalty= 4.6
CG311 CG311 CG311 OG301 0.3900 2 0.00 ! LIG , from OG301 CG311 CG321 CG321, penalty= 4.6
CG311 CG311 CG311 OG303 0.2000 3 180.00 ! LIG , from CG311 CG311 CG321 OG303, penalty= 4
CG331 CG311 CG311 OG303 0.2000 3 180.00 ! LIG , from CG321 CG311 CG321 OG303, penalty= 4.9
OG301 CG311 CG311 OG303 0.2000 3 0.00 ! LIG , from OG302 CG311 CG321 OG303, penalty= 4.5
OG301 CG311 CG311 OG311 0.2000 3 0.00 ! LIG , from OG311 CG311 CG321 OG303, penalty= 5.5
OG303 CG311 CG311 OG311 0.2000 3 0.00 ! LIG , from OG311 CG311 CG321 OG303, penalty= 4
OG303 CG311 CG311 HGA1 0.1950 3 0.00 ! LIG , from OG301 CG311 CG311 HGA1, penalty= 3
CG311 CG311 CG321 OG301 0.2000 3 180.00 ! LIG , from CG321 CG311 CG321 OG302, penalty= 1.1
OG311 CG311 CG321 OG301 0.2000 3 0.00 ! LIG , from OG311 CG311 CG321 OG303, penalty= 1.5
HGA1 CG311 CG321 OG301 0.1950 3 0.00 ! LIG , from HGA1 CG311 CG321 OG302, penalty= 0.5
CG311 CG311 OG301 CG321 0.4000 1 0.00 ! LIG , from CG311 CG311 OG301 CG331, penalty= 0.9
CG311 CG311 OG301 CG321 0.4900 3 0.00 ! LIG , from CG311 CG311 OG301 CG331, penalty= 0.9
HGA1 CG311 OG301 CG321 0.2840 3 0.00 ! LIG , from HGA1 CG311 OG301 CG331, penalty= 0.9
CG311 CG311 OG303 SG3O2 0.0000 3 0.00 ! LIG , from CG321 CG321 OG303 SG3O1, penalty= 9.6
HGA1 CG311 OG303 SG3O2 0.0000 3 0.00 ! LIG , from HGA2 CG321 OG303 SG3O1, penalty= 9
CG2O4 CG311 OG311 HGP1 0.3500 1 0.00 ! LIG , from CG2O5 CG311 OG311 HGP1, penalty= 0.5
CG2O4 CG311 OG311 HGP1 0.3700 2 0.00 ! LIG , from CG2O5 CG311 OG311 HGP1, penalty= 0.5
CG2O4 CG311 OG311 HGP1 0.0100 3 180.00 ! LIG , from CG2O5 CG311 OG311 HGP1, penalty= 0.5
CG311 CG321 OG301 CG311 0.5700 1 0.00 ! LIG , from CG321 CG321 OG301 CG321, penalty= 1.2
CG311 CG321 OG301 CG311 0.2900 2 0.00 ! LIG , from CG321 CG321 OG301 CG321, penalty= 1.2
CG311 CG321 OG301 CG311 0.4300 3 0.00 ! LIG , from CG321 CG321 OG301 CG321, penalty= 1.2
HGA2 CG321 OG301 CG311 0.2840 3 0.00 ! LIG , from HGA2 CG321 OG301 CG321, penalty= 0.6
CG311 OG303 SG3O2 OG2P1 0.3000 3 0.00 ! LIG , from CG331 OG303 SG3O2 OG2P1, penalty= 1.5
CG311 OG303 SG3O2 OG311 1.8000 1 180.00 ! LIG , from CG331 OG303 SG3O2 NG321, penalty= 35.7
CG311 OG303 SG3O2 OG311 0.5000 2 0.00 ! LIG , from CG331 OG303 SG3O2 NG321, penalty= 35.7
CG311 OG303 SG3O2 OG311 0.4000 3 0.00 ! LIG , from CG331 OG303 SG3O2 NG321, penalty= 35.7
HGP1 OG311 SG3O2 OG2P1 0.3000 3 0.00 ! LIG , from HGP1 OG311 PG1 OG2P1, penalty= 200
HGP1 OG311 SG3O2 OG303 1.6000 1 180.00 ! LIG , from HGP1 OG311 PG1 OG303, penalty= 200
HGP1 OG311 SG3O2 OG303 0.9000 2 0.00 ! LIG , from HGP1 OG311 PG1 OG303, penalty= 200
IMPROPERS
END
RETURN