Then, user can submit the structure and download the NAMD files, i.e BNZ.prm (coordinate file) and BNZ.rtp (topology) files. If the ligand submitted is not neutral, just CM1A model can be applied (the charge must be specified by the user) and the scale factor 1.14 will not be used. Optimization will perform a quick minimization of the submitted structure using the OPLS-AA and the charge model parameters generated by the server. For protein-ligand simulation, before uploading, make sure that ligand residue number is changed to 1 (BOSS, the core of LigParGen server, only works for a limited number of residues).īefore to submit the structure to the server, user must specify two options: optimization and charge model (1.14*CM1A or 1.14*CM1A-LBCC). Upload the ligand_wH.pdb to LigParGen server to get the parameter files. Make sure that the right number of hydrogens are added and the ligand charge matches the expected value.
This produces protein_clean.pdb and ligand_wH.pdb that will be used further. Chimera -nogui -script "prep_prot_lig.py 4w52.pdb BNZ" Make sure you have Chimera installed and can be called from Command Prompt. Midas.write(ligand, None, "ligand_wH.pdb") Midas.write(protein, None, "protein_clean.pdb") Prep(protein,addHFunc = None,addCharges = False)
Os.system( 'grep ATOM %s > %s _clean.pdb' %(PDB_file,PDB_file)) # PDB_FILE SHOULD THE COMPLETE PATH OF THE FILE # REPLACE BNZ with LIGAND resname # USAGE: Chimera -nogui -script "prep_prot_lig.py 4w52.pdb BNZ" import chimera
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