Disulfide.txt
From Rizzo_Lab
# (3) Read topology file
topology toppar/top_all22_prot.inp
# (4) Build protein segment
segment BPTI {
29
pdb output/6PTI_protein.pdb
}
# (5) Patch protein segment
patch DISU BPTI:5 BPTI:55
patch DISU BPTI:14 BPTI:38
patch DISU BPTI:30 BPTI:51
# (6) Read protein coordinates from PDB file
pdbalias atom ILE CD1 CD ; # formerly "alias atom ..."
coordpdb output/6PTI_protein.pdb BPTI
# (7) Build water segment
pdbalias residue HOH TIP3 ; # formerly "alias residue ..."
segment SOLV {
auto none
pdb output/6PTI_water.pdb
}
# (8) Read water coordinaes from PDB file
pdbalias atom HOH O OH2 ; # formerly "alias atom ..."
coordpdb output/6PTI_water.pdb SOLV
# (9) Guess missing coordinates
guesscoord
# (10) Write structure and coordinate files
writepsf output/bpti.psf
writepdb output/bpti.pdb
# End of psfgen commands
