PSFGEN from NAMD 2.5 for Linux-i686
reading topology file top_all27_prot_lipid.inp

>>>>>> Combined CHARMM All-Hydrogen Topology File for <<<<<<<<<
>>>>>>>>> CHARMM22 Proteins and CHARMM27 Lipids <<<<<<<<<<
from
>>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<<
>>>>>>>>>>>>>>>>>>>>> August 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<
>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<
>>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu  <<<<<<<<<
and
  \\\\\\\ CHARMM27 All-Hydrogen Lipid Topology File ///////
  \\\\\\\\\\\\\\\\\\ Developmental /////////////////////////
              Alexander D. MacKerell Jr.
                     August 1999
 All comments to ADM jr.  email: alex,mmiris.ab.umd.edu
              telephone: 410-706-7442

Created by CHARMM version 27 1
reading topology file top_unbonded_zincs.inp

  zinc and such,... 

Created by CHARMM version 21 1
reading topology file top_PTR.inp

Created by CHARMM version 21 1
reading topology file top_SO4.inp

Created by CHARMM version 22 1
aliasing residue ZN to ZNR
aliasing residue HIS to HSE
aliasing residue DLE to LEU
aliasing residue DVA to VAL
aliasing residue ETA atom O to OG
aliasing residue ILE atom CD1 to CD
aliasing residue PTR to TYR
building segment C
reading residues from pdb file chainC.pdb
extracted 144 residues from pdb file
Info: generating structure...
Info: skipping improper N-C-CA-HN at beginning of segment.
Info: skipping conformation C-N-CA-C at beginning of segment.
Info: skipping conformation C-CA-N-HN at beginning of segment.
Info: skipping bond C-N at end of segment.
Info: skipping improper C-CA-N-O at end of segment.
Info: skipping conformation CA-C-N-CA at end of segment.
Info: skipping conformation N-CA-C-O at end of segment.
Info: skipping conformation N-CA-C-N at end of segment.
Info: segment complete.
reading coordinates from pdb file chainC.pdb for segment C
Warning: failed to set coordinate for atom O	 TYR:1147	  C
building segment B
disabling angle autogeneration
disabling dihedral autogeneration
setting patch for first residue to NONE
setting patch for last residue to NONE
reading residues from pdb file chainB.pdb
extracted 9 residues from pdb file
Info: generating structure...
Info: skipping improper N-C-CA-HN at beginning of segment.
Info: skipping conformation C-N-CA-C at beginning of segment.
Info: skipping conformation C-CA-N-HN at beginning of segment.
Info: skipping bond C-N at end of segment.
Info: skipping improper C-CA-N-O at end of segment.
Info: skipping conformation CA-C-N-CA at end of segment.
Info: skipping conformation N-CA-C-O at end of segment.
Info: skipping conformation N-CA-C-N at end of segment.
Info: segment complete.
reading coordinates from pdb file chainB.pdb for segment B
Warning: failed to set coordinate for atom P	 PTR:7	  B
Warning: failed to set coordinate for atom O1P	 PTR:7	  B
Warning: failed to set coordinate for atom O2P	 PTR:7	  B
Warning: failed to set coordinate for atom O3P	 PTR:7	  B
Warning: failed to set coordinate for atom OXT	 ALA:12	  B
applying patch PT1 to 1 residues
unknown patch type PT1
ERROR: failed to apply patch
building segment A
reading residues from pdb file chainA.pdb
extracted 388 residues from pdb file
Info: generating structure...
Info: skipping improper N-C-CA-CD at beginning of segment.
Info: skipping conformation C-N-CA-C at beginning of segment.
Info: skipping conformation C-CA-N-CD at beginning of segment.
Info: skipping bond C-N at end of segment.
Info: skipping improper C-CA-N-O at end of segment.
Info: skipping conformation CA-C-N-CA at end of segment.
Info: skipping conformation N-CA-C-O at end of segment.
Info: skipping conformation N-CA-C-N at end of segment.
Info: segment complete.
reading coordinates from pdb file chainA.pdb for segment A
Warning: failed to set coordinate for atom O	 PHE:434	  A
Warning: failed to set coordinate for atom OXT	 PHE:434	  A
building segment ZN
reading residues from pdb file ions.pdb
extracted 7 residues from pdb file
Info: generating structure...
Info: segment complete.
reading coordinates from pdb file ions.pdb for segment ZN
Info: guessing coordinates for 4409 atoms (37 non-hydrogen)
Warning: poorly guessed coordinates for 10 atoms (4 non-hydrogen):
Warning: poorly guessed coordinate for atom HT1	 SER:1004	  C
Warning: poorly guessed coordinate for atom HT2	 SER:1004	  C
Warning: poorly guessed coordinate for atom HT3	 SER:1004	  C
Warning: poorly guessed coordinate for atom OT1	 TYR:1147	  C
Warning: poorly guessed coordinate for atom OT2	 TYR:1147	  C
Warning: poorly guessed coordinate for atom HN	 SER:4	  B
Warning: poorly guessed coordinate for atom HN1	 PRO:47	  A
Warning: poorly guessed coordinate for atom HN2	 PRO:47	  A
Warning: poorly guessed coordinate for atom OT1	 PHE:434	  A
Warning: poorly guessed coordinate for atom OT2	 PHE:434	  A
Info: writing psf file protein.psf
total of 8794 atoms
total of 8901 bonds
total of 15919 angles
total of 23409 dihedrals
total of 1426 impropers
Info: psf file complete.
Info: writing pdb file protein.pdb
Info: Atoms with guessed coordinates will have occupancy of 0.0.
Info: pdb file complete.