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***   Demonstration of psfgen - NAMD psf file generator   ***
***   Please read comments in script for more details!    ***
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*** creating output directory ***
*** splitting input PDB file into segments ***
*** reading topology file ***
reading topology file top_all22_prot.inp

>>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<
>>>>>>>>>>>>>>>>>>>>>>> July 1997 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<
>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<
>>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu  <<<<<<<<<

Created by CHARMM version 22 1
*** building segment BPTI ***
building segment BPTI
reading residues from pdb file output/6PTI_protein.pdb
extracted 57 residues from pdb file
generating structure at end of segment
add improper failed in residue ARG:1
add conformation failed in residue ARG:1
add conformation failed in residue ARG:1
add bond C(0) N(1) failed in residue GLY:57
add improper failed in residue GLY:57
add conformation failed in residue GLY:57
add conformation failed in residue GLY:57
add conformation failed in residue GLY:57
*** adding patches ***
applying patch DISU to 2 residues
applying patch DISU to 2 residues
applying patch DISU to 2 residues
*** writing psf structure file ***
writing psf file output/bpti.psf
total of 882 atoms
total of 896 bonds
total of 1608 angles
total of 2366 dihedrals
total of 139 impropers
*** reading coordinates from pdb file ***
aliasing residue ILE atom CD1 to CD
reading coordinates from pdb file output/6PTI_protein.pdb for segment BPTI
*** guessing missing coordinates ***
guessing coordinates based on topology file
Warning: guessing coordinates for 437 atoms
Warning: poorly guessed coordinates for 5 atoms
*** writing pdb coordinate file ***
writing pdb file output/bpti.pdb
*** advanced demo begins here ***
*** adding a segment of water ***
aliasing residue HOH to TIP3
building segment SOLV
disabling angle autogeneration
disabling dihedral autogeneration
reading residues from pdb file output/6PTI_water.pdb
extracted 73 residues from pdb file
generating structure at end of segment
*** reading water coordinates ***
aliasing residue HOH atom O to OH2
reading coordinates from pdb file output/6PTI_water.pdb for segment SOLV
*** guessing water coordinates - not possible ***
guessing coordinates based on topology file
Warning: guessing coordinates for 583 atoms
Warning: poorly guessed coordinates for 5 atoms
Warning: failed to guess coordinates for 146 atoms