# psfgen input generated by Py-ChemShell

# read in topology file
topology /home/ylu/chemsh/parameterise/chemsh/data/charmm/c36_jul18/top_all36_prot.rtf

# build ATOM segment
segment ATOM {
    pdb _segment_ATOM.pdb
}

# automatic residue patch generated by ChemShell
patch DISU ATOM:14 ATOM:38
patch DISU ATOM:5 ATOM:55
patch DISU ATOM:30 ATOM:51

# automatic alias generated by ChemShell
pdbalias atom ILE CD1 CD;

# read ATOM coordinates from PDB file
coordpdb _segment_ATOM.pdb ATOM

# read in topology file
topology /home/ylu/chemsh/parameterise/tests/namd/6pti/toppar_water_ions_namd.str

# residue aliases specified via `residue_aliases`
pdbalias residue HOH TIP3;

# build HETATM segment
segment HETATM {
    auto none
    pdb _segment_HETATM.pdb
}

# automatic alias generated by ChemShell
pdbalias atom b'HOH' O OH2;

# read HETATM coordinates from PDB file
coordpdb _segment_HETATM.pdb HETATM

# guess missing coordinate
guesscoord

# write out PSF and PDB files
writepsf _output/6PTI.psf
writepdb _output/6PTI.pdb
