Hi,
In ubuntu I can’t use anaconda because it messed my config. I install bioexcel the native way ubuntu python. It seems to work except I have problems with gromacs
fixed_pdb = pdbCode + “_fixed.pdb”
Create and launch bb
FixSideChain(input_pdb_path=downloaded_pdb,
output_pdb_path=fixed_pdb).launch()
!grep -v HOH 1AKI.pdb > 1AKI_fixed.pdb
I have to create namually the file, can you help me fixing that ?
Here too :
from biobb_chemistry.acpype.acpype_params_gmx import AcpypeParamsGMX
Create prop dict and inputs/outputs
output_acpype_gro = ligandCode + ‘params.gro’
output_acpype_itp = ligandCode + ‘params.itp’
output_acpype_top = ligandCode + ‘params.top’
output_acpype = ligandCode + ‘params’
prop = {
‘basename’ : output_acpype,
‘charge’ : mol_charge
}
#Create and launch bb
AcpypeParamsGMX(input_path=output_babel_min,
output_path_gro=output_acpype_gro,
output_path_itp=output_acpype_itp,
output_path_top=output_acpype_top,
properties=prop).launch()
It seems to be a problem with path in bash ?
amber20 and gromacs work perfect I have done many tutorials.
If I can fix it and translate le tutorial in french would it be of interest for you ?
best regards
Henri