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40 lines
1.6 KiB
40 lines
1.6 KiB
2 years ago
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import os
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def proprep(protein):
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filename = protein.split('.pdb')[0]
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os.system('$GROMACS_DIR/gmx pdb2gmx -f {} -o {}.gro'.format(protein,filename))
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def ligprep(ligand,charge):
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if '.mol2' in ligand:
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filename = ligand.split('.mol2')[0]
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os.system('obabel {} -O temp_{}_h.pdb'.format(ligand,filename))
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elif '.xyz' in ligand:
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filename = ligand.split('.xyz')[0]
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os.system('obabel {} -O temp_{}_h.pdb'.format(ligand,filename))
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elif '.pdb' in ligand:
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filename = ligand.split('.pdb')[0]
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os.system('reduce {}.pdb > temp_{}_h.pdb'.format(filename,filename))
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delete_entries = ['CONECT']
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with open('temp_{}_h.pdb'.format(filename),'r') as oldpdb, open('{}_h.pdb'.format(filename),'w') as newpdb:
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for line in oldpdb:
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if not any(del_entry in line for del_entry in delete_entries):
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newpdb.write(line)
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os.system('rm temp_{}_h.pdb'.format(filename))
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os.system('antechamber -j 5 -at gaff -dr no -i {}_h.pdb -fi pdb -o {}_h.mol2 -fo mol2 -c gas -s 2 -nc {}'.format(filename,filename,charge))
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os.system('parmchk2 -i {}_h.mol2 -f mol2 -o {}_h.frcmod'.format(filename,filename))
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with open('tleap.in','w') as f:
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print("""source oldff/leaprc.ff99SB
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source leaprc.gaff
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LIG = loadmol2 {}_h.mol2
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loadamberparams {}_h.frcmod
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check LIG
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saveoff LIG {}_h.lib
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saveamberparm LIG {}_h.prmtop {}_h.inpcrd
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quit""".format(filename,filename,filename,filename,filename),file=f)
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os.system('tleap -f tleap.in')
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os.system('acpype -p {}_h.prmtop -x {}_h.inpcrd'.format(filename,filename))
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