GROMACS version: 2025
GROMACS modification: No
Operating System: Ubuntu 24.04
Hello!
I am a new user trying to learn Gromacs from Lemkul Labs’ GROMACS tutorial on Protein-Ligand. During conversion from CHARMM topology to Gromacs using the charmm2gmx python code for the ligand, I encountered an error as seen below.
python ~/mdynamics/cgenff_charmm2gmx/cgenff_charmm2gmx.py 17AAG clean_ligand.cgenff.mol2 clean_ligand_fixed.str ~/mdynamics/cgenff_charmm2gmx/charmm36-jul2022.ff
NOTE 1: Code tested with Python 3.12 Your version: 3.12.0 | packaged by conda-forge | (main, Oct 3 2023, 08:43:22) [GCC 12.3.0]
NOTE 2: Code tested with NetworkX 3.4.2. Your version: 3.4.2
NOTE 3: Please be sure to use the same version of CGenFF in your simulations that was used during parameter generation:
–Version of CGenFF detected in clean_ligand_fixed.str : 4.6
–Version of CGenFF detected in /home/lab/mdynamics/cgenff_charmm2gmx/charmm36-jul2022.ff/forcefield.doc : 4.6
NOTE 4: To avoid duplicated parameters, do NOT select the ‘Include parameters that are already in CGenFF’ option when uploading a molecule into CGenFF.
Traceback (most recent call last):
File “/home/lab/mdynamics/cgenff_charmm2gmx/cgenff_charmm2gmx.py”, line 1104, in
main()
File “/home/lab/mdynamics/cgenff_charmm2gmx/cgenff_charmm2gmx.py”, line 1079, in main
params = parse_charmm_parameters(prmlines)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/home/lab/mdynamics/cgenff_charmm2gmx/cgenff_charmm2gmx.py”, line 278, in parse_charmm_parameters
raise ValueError(
ValueError: ERROR: Incorrect number of values found in ANGL section
I tried to verify if I installed it correctly by running the test data which produced the successful message. However, I noticed my .mol2 files has some line in the ANGLE section while the test data are empty. This was in my files.
ANGLES
CG311 CG2D1 CG331 48.00 123.50 ! 17AAG , from CG321 CG2D1 CG331, penalty= 0.6
CG2O5 CG2D1O NG2S1 78.65 120.66 ! 17AAG , from CG2O1 CG2D1O NG2S1, penalty= 3
CG2O5 CG2D1O NG311 68.61 111.88 ! 17AAG , from CG2O5 CG2D1O OG311, penalty= 38
CG2O1 CG2DC1 CG331 65.00 123.50 ! 17AAG , from CG2O1 CG2DC2 CG321, penalty= 0.9
CG2DC2 CG2DC2 CG311 48.00 123.50 ! 17AAG , from CG2DC1 CG2DC1 CG321, penalty= 0.6
CG311 CG2DC2 HGA4 40.00 116.00 ! 17AAG , from CG321 CG2DC1 HGA4, penalty= 0.6
NG2S2 CG2O6 OG302 90.00 110.30 ! 17AAG , from NG2S1 CG2O6 OG302, penalty= 1
CG2D1 CG311 CG311 32.00 112.20 ! 17AAG , from CG2D1 CG311 CG321, penalty= 0.6
CG2D1 CG311 CG331 32.00 112.20 ! 17AAG , from CG2D1 CG311 CG321, penalty= 0.9
CG2D1 CG311 OG302 20.00 99.00 ! 17AAG , from CG2DC1 CG321 OG3R60, penalty= 11.7
CG2DC2 CG311 CG311 32.00 112.20 ! 17AAG , from CG2D1 CG311 CG321, penalty= 1.1
CG2DC2 CG311 OG301 20.00 99.00 ! 17AAG , from CG2DC1 CG321 OG3R60, penalty= 11.2
CG2DC2 CG311 HGA1 45.00 111.50 ! 17AAG , from CG2D1 CG311 HGA1, penalty= 0.5
CG311 CG311 OG302 115.00 109.70 ! 17AAG , from CG311 CG311 OG301, penalty= 0.5
CG2DC1 CG321 CG311 32.00 112.20 ! 17AAG , from CG2D1 CG321 CG311, penalty= 0.5
CG2D1O NG311 CG321 70.00 121.70 ! 17AAG , from CG2D2O NG301 CG3C51, penalty= 16.4
CG2O6 OG302 CG311 40.00 111.00 ! 17AAG , from CG2O6 OG302 CG321, penalty= 0.6
I would appreciate any input regarding my error and what I can do to proceed.
Thank you very much.