Extending the receptor-ligand tutorial to cofactors and metals?

BioBB
8

Thank you Adam!

I did this:

from biobb_md.gromacs.pdb2gmx import Pdb2gmx

Create inputs/outputs

output_pdb2gmx_gro = pdbCode+‘_pdb2gmx.gro’
output_pdb2gmx_top_zip = pdbCode+‘_pdb2gmx_top.zip’
prop = {
‘force_field’ : ‘amber99sb’,
‘water_type’: ‘spce’,
‘gmxlib’ :‘/Applications/anaconda3/envs/biobb_Protein-Complex_MDsetup_tutorial/share/gromacs/top/’,
‘gmx_path’:‘/Applications/anaconda3/envs/biobb_Protein-Complex_MDsetup_tutorial/bin/gmx’
}

Create and launch bb

Pdb2gmx(input_pdb_path=fixed_pdb,
output_gro_path=output_pdb2gmx_gro,
output_top_zip_path=output_pdb2gmx_top_zip,
properties=prop).launch()

and got this error:

Inconsistency in user input:
Force field ‘amber99sb’ occurs in 2 places, but not in the current directory.
Run without the -ff switch and select the force field interactively.

I don´t understand what´s the problem as amber99sb.ff is in the gmxlib path and here is also the modified specbond.dat file.
Any clues?
Thank you!
Juan