Galaxy | BIOBB | Published Workflow | GMX ligand parameterization

GMX ligand parameterization

Annotation:

Step	Annotation
Step 1: Ligand output PDB name myligand.pdb Take tool settings: Manual Input Properties Input: ligand_code IBP api_id mmb - MMB PDB mirror API
Step 2: BabelAddHydrogens input DAT,ENT,FA,FASTA,GRO,INP,LOG,MCIF,MDL,MMCIF,MOL,MOL2,PDB,PDBQT,PNG,SDF,SMI,SMILES,TXT,XML,XTC file Output dataset 'output_pdb_path' from step 1 output ENT,FA,FASTA,GRO,INP,MCIF,MDL,MMCIF,MOL,MOL2,PDB,PDBQT,PNG,SDF,SMI,SMILES,TXT name mybabel_add_hydrogens.mol2 Take tool settings: Manual Input Properties Input: input_format pdb - Protein Data Bank format output_format mol2 - Complete and portable representation of a SYBYL molecule coordinates 3 - 3D coordinates ph 7.4 binary_path obabel
Step 3: BabelMinimize input PDB,MOL2 file Output dataset 'output_path' from step 2 output PDB,MOL2 name mybabel_minimize.pdb Take tool settings: Manual Input Properties Input: criteria 1e-10 method sd - steepest descent algorithm force_field GAFF - General Amber Force Field hydrogens False steps 2500 cutoff False rvdw 6.0 rele 10.0 frequency 10 binary_path obminimize output_format pdb
Step 4: AcpypeParamsGmx input PDB,MDL,MOL2 file Output dataset 'output_path' from step 3 output GRO name myacpype_params_gmx.gro output ITP name myacpype_params_gmx.itp output TOP name myacpype_params_gmx.top Take tool settings: Manual Input Properties Input: basename IBPparams charge 0 binary_path acpype

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gbayarri

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