reading topology file parameters/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 reading topology file parameters/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 aliasing residue HIS to HSD aliasing residue ILE atom CD1 to CD building segment SEG0 reading residues from pdb file myfile_frag0.pdb aliasing residue HIS to HSD aliasing residue ILE atom CD1 to CD building segment SEG0 reading residues from pdb file myfile_frag0.pdb extracted 26 residues from pdb file generating structure at end of segment no residue 1 before GLU:698 of segment SEG0 Warning: add improper failed in residue GLU:698 no residue 1 before GLU:698 of segment SEG0 Warning: add conformation C-N-CA-C failed in residue GLU:698 no residue 1 before GLU:698 of segment SEG0 Warning: add conformation C-CA-N-HN failed in residue GLU:698 extracted 26 residues from pdb file generating structure at end of segment no residue 1 before GLU:698 of segment SEG0 Warning: add improper failed in residue GLU:698 no residue 1 before GLU:698 of segment SEG0 Warning: add conformation C-N-CA-C failed in residue GLU:698 no residue 1 before GLU:698 of segment SEG0 Warning: add conformation C-CA-N-HN failed in residue GLU:698 no residue 1 past GLY:723 of segment SEG0 Warning: add bond C(0) N(1) failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add improper failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation CA-C-N-CA failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation N-CA-C-O failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation N-CA-C-N failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 reading coordinates from pdb file myfile_frag0.pdb for segment SEG0 Warning: add bond C(0) N(1) failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add improper failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation CA-C-N-CA failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation N-CA-C-O failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation N-CA-C-N failed in residue GLY:723 reading coordinates from pdb file myfile_frag0.pdb for segment SEG0 no atom O in residue GLY:723 of segment SEG0 Warning: failed to set coordinate for atom O in residue GLY:723 of segment SEG0 building segment SEG1 reading residues from pdb file myfile_frag1.pdb no atom O in residue GLY:723 of segment SEG0 Warning: failed to set coordinate for atom O in residue GLY:723 of segment SEG0 building segment SEG1 reading residues from pdb file myfile_frag1.pdb extracted 31 residues from pdb file generating structure at end of segment no residue 1 before GLY:654 of segment SEG1 Warning: add improper failed in residue GLY:654 no residue 1 before GLY:654 of segment SEG1 Warning: add conformation C-N-CA-C failed in residue GLY:654 no residue 1 before GLY:654 of segment SEG1 Warning: add conformation C-CA-N-HN failed in residue GLY:654 extracted 31 residues from pdb file generating structure at end of segment no residue 1 before GLY:654 of segment SEG1 no residue 1 past SER:684 of segment SEG1 Warning: add improper failed in residue GLY:654 no residue 1 before GLY:654 of segment SEG1 Warning: add conformation C-N-CA-C failed in residue GLY:654 no residue 1 before GLY:654 of segment SEG1 Warning: add conformation C-CA-N-HN failed in residue GLY:654 Warning: add bond C(0) N(1) failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add improper failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation CA-C-N-CA failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation N-CA-C-O failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation N-CA-C-N failed in residue SER:684 reading coordinates from pdb file myfile_frag1.pdb for segment SEG1 no residue 1 past SER:684 of segment SEG1 Warning: add bond C(0) N(1) failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add improper failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation CA-C-N-CA failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation N-CA-C-O failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation N-CA-C-N failed in residue SER:684 reading coordinates from pdb file myfile_frag1.pdb for segment SEG1 no atom O in residue SER:684 of segment SEG1 Warning: failed to set coordinate for atom O in residue SER:684 of segment SEG1 building segment SEG2 reading residues from pdb file myfile_frag2.pdb extracted 6 residues from pdb file generating structure at end of segment no residue 1 before ARG:630 of segment SEG2 Warning: add improper failed in residue ARG:630 no residue 1 before ARG:630 of segment SEG2 Warning: add conformation C-N-CA-C failed in residue ARG:630 no residue 1 before ARG:630 of segment SEG2 Warning: add conformation C-CA-N-HN failed in residue ARG:630 no residue 1 past PRO:635 of segment SEG2 Warning: add bond C(0) N(1) failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add improper failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation CA-C-N-CA failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation N-CA-C-O failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation N-CA-C-N failed in residue PRO:635 reading coordinates from pdb file myfile_frag2.pdb for segment SEG2 no atom O in residue SER:684 of segment SEG1 Warning: failed to set coordinate for atom O in residue SER:684 of segment SEG1 building segment SEG2 reading residues from pdb file myfile_frag2.pdb no atom O in residue PRO:635 of segment SEG2 extracted 6 residues from pdb file Warning: failed to set coordinate for atom O in residue PRO:635 of segment SEG2 building segment SEG3 reading residues from pdb file myfile_frag3.pdb generating structure at end of segment no residue 1 before ARG:630 of segment SEG2 Warning: add improper failed in residue ARG:630 no residue 1 before ARG:630 of segment SEG2 Warning: add conformation C-N-CA-C failed in residue ARG:630 no residue 1 before ARG:630 of segment SEG2 Warning: add conformation C-CA-N-HN failed in residue ARG:630 no residue 1 past PRO:635 of segment SEG2 Warning: add bond C(0) N(1) failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add improper failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation CA-C-N-CA failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation N-CA-C-O failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation N-CA-C-N failed in residue PRO:635 reading coordinates from pdb file myfile_frag2.pdb for segment SEG2 no atom O in residue PRO:635 of segment SEG2 Warning: failed to set coordinate for atom O in residue PRO:635 of segment SEG2 building segment SEG3 reading residues from pdb file myfile_frag3.pdb extracted 105 residues from pdb file generating structure at end of segment no residue 1 before PHE:560 of segment SEG3 Warning: add improper failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG3 Warning: add conformation C-N-CA-C failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG3 Warning: add conformation C-CA-N-HN failed in residue PHE:560 extracted 105 residues from pdb file generating structure at end of segment no residue 1 before PHE:560 of segment SEG3 Warning: add improper failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG3 Warning: add conformation C-N-CA-C failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG3 Warning: add conformation C-CA-N-HN failed in residue PHE:560 no residue 1 past GLU:664 of segment SEG3 Warning: add bond C(0) N(1) failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add improper failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation CA-C-N-CA failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation N-CA-C-O failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation N-CA-C-N failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add bond C(0) N(1) failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add improper failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation CA-C-N-CA failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation N-CA-C-O failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation N-CA-C-N failed in residue GLU:664 reading coordinates from pdb file myfile_frag3.pdb for segment SEG3 no atom O in residue GLU:664 of segment SEG3 Warning: failed to set coordinate for atom O in residue GLU:664 of segment SEG3 building segment SEG4 reading residues from pdb file myfile_frag4.pdb reading coordinates from pdb file myfile_frag3.pdb for segment SEG3 no atom O in residue GLU:664 of segment SEG3 Warning: failed to set coordinate for atom O in residue GLU:664 of segment SEG3 building segment SEG4 reading residues from pdb file myfile_frag4.pdb reading topology file parameters/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 aliasing residue HIS to HSD aliasing residue ILE atom CD1 to CD building segment SEG0 reading residues from pdb file myfile_frag0.pdb extracted 26 residues from pdb file reading topology file parameters/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 generating structure at end of segment no residue 1 before GLU:698 of segment SEG0 Warning: add improper failed in residue GLU:698 no residue 1 before GLU:698 of segment SEG0 Warning: add conformation C-N-CA-C failed in residue GLU:698 no residue 1 before GLU:698 of segment SEG0 Warning: add conformation C-CA-N-HN failed in residue GLU:698 extracted 416 residues from pdb file generating structure at end of segment no residue 1 past GLY:723 of segment SEG0 Warning: add bond C(0) N(1) failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add improper failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation CA-C-N-CA failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation N-CA-C-O failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation N-CA-C-N failed in residue GLY:723 reading coordinates from pdb file myfile_frag0.pdb for segment SEG0 extracted 416 residues from pdb file generating structure at end of segment no atom O in residue GLY:723 of segment SEG0 no residue 1 before HSD:134 of segment SEG4 Warning: failed to set coordinate for atom O in residue GLY:723 of segment SEG0 building segment SEG1 reading residues from pdb file myfile_frag1.pdb Warning: add improper failed in residue HSD:134 no residue 1 before HSD:134 of segment SEG4 Warning: add conformation C-N-CA-C failed in residue HSD:134 no residue 1 before HSD:134 of segment SEG4 Warning: add conformation C-CA-N-HN failed in residue HSD:134 aliasing residue HIS to HSD aliasing residue ILE atom CD1 to CD building segment SEG0 reading residues from pdb file myfile_frag0.pdb extracted 31 residues from pdb file generating structure at end of segment no residue 1 before GLY:654 of segment SEG1 Warning: add improper failed in residue GLY:654 no residue 1 before GLY:654 of segment SEG1 Warning: add conformation C-N-CA-C failed in residue GLY:654 no residue 1 before GLY:654 of segment SEG1 Warning: add conformation C-CA-N-HN failed in residue GLY:654 no residue 1 before HSD:134 of segment SEG4 Warning: add improper failed in residue HSD:134 no residue 1 before HSD:134 of segment SEG4 Warning: add conformation C-N-CA-C failed in residue HSD:134 no residue 1 before HSD:134 of segment SEG4 Warning: add conformation C-CA-N-HN failed in residue HSD:134 extracted 26 residues from pdb file generating structure at end of segment no residue 1 past SER:684 of segment SEG1 Warning: add bond C(0) N(1) failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add improper failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation CA-C-N-CA failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation N-CA-C-O failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation N-CA-C-N failed in residue SER:684 no residue 1 before GLU:698 of segment SEG0 Warning: add improper failed in residue GLU:698 no residue 1 before GLU:698 of segment SEG0 Warning: add conformation C-N-CA-C failed in residue GLU:698 no residue 1 before GLU:698 of segment SEG0 Warning: add conformation C-CA-N-HN failed in residue GLU:698 reading coordinates from pdb file myfile_frag1.pdb for segment SEG1 no residue 1 past GLY:723 of segment SEG0 Warning: add bond C(0) N(1) failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add improper failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation CA-C-N-CA failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation N-CA-C-O failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation N-CA-C-N failed in residue GLY:723 no atom O in residue SER:684 of segment SEG1 Warning: failed to set coordinate for atom O in residue SER:684 of segment SEG1 building segment SEG2 reading residues from pdb file myfile_frag2.pdb extracted 6 residues from pdb file reading coordinates from pdb file myfile_frag0.pdb for segment SEG0 generating structure at end of segment no residue 1 before ARG:630 of segment SEG2 Warning: add improper failed in residue ARG:630 no residue 1 before ARG:630 of segment SEG2 Warning: add conformation C-N-CA-C failed in residue ARG:630 no residue 1 before ARG:630 of segment SEG2 Warning: add conformation C-CA-N-HN failed in residue ARG:630 no residue 1 past PRO:635 of segment SEG2 Warning: add bond C(0) N(1) failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add improper failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation CA-C-N-CA failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation N-CA-C-O failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation N-CA-C-N failed in residue PRO:635 reading coordinates from pdb file myfile_frag2.pdb for segment SEG2 no atom O in residue PRO:635 of segment SEG2 Warning: failed to set coordinate for atom O in residue PRO:635 of segment SEG2 building segment SEG3 reading residues from pdb file myfile_frag3.pdb no atom O in residue GLY:723 of segment SEG0 Warning: failed to set coordinate for atom O in residue GLY:723 of segment SEG0 building segment SEG1 reading residues from pdb file myfile_frag1.pdb extracted 31 residues from pdb file generating structure at end of segment no residue 1 before GLY:654 of segment SEG1 Warning: add improper failed in residue GLY:654 no residue 1 before GLY:654 of segment SEG1 Warning: add conformation C-N-CA-C failed in residue GLY:654 no residue 1 before GLY:654 of segment SEG1 Warning: add conformation C-CA-N-HN failed in residue GLY:654 no residue 1 past SER:684 of segment SEG1 Warning: add bond C(0) N(1) failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add improper failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation CA-C-N-CA failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation N-CA-C-O failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation N-CA-C-N failed in residue SER:684 reading coordinates from pdb file myfile_frag1.pdb for segment SEG1 extracted 105 residues from pdb file generating structure at end of segment no residue 1 before PHE:560 of segment SEG3 Warning: add improper failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG3 Warning: add conformation C-N-CA-C failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG3 Warning: add conformation C-CA-N-HN failed in residue PHE:560 no atom O in residue SER:684 of segment SEG1 Warning: failed to set coordinate for atom O in residue SER:684 of segment SEG1 building segment SEG2 reading residues from pdb file myfile_frag2.pdb extracted 6 residues from pdb file generating structure at end of segment no residue 1 before ARG:630 of segment SEG2 Warning: add improper failed in residue ARG:630 no residue 1 before ARG:630 of segment SEG2 Warning: add conformation C-N-CA-C failed in residue ARG:630 no residue 1 before ARG:630 of segment SEG2 Warning: add conformation C-CA-N-HN failed in residue ARG:630 no residue 1 past PRO:635 of segment SEG2 Warning: add bond C(0) N(1) failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add improper failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation CA-C-N-CA failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation N-CA-C-O failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation N-CA-C-N failed in residue PRO:635 reading coordinates from pdb file myfile_frag2.pdb for segment SEG2 no atom O in residue PRO:635 of segment SEG2 Warning: failed to set coordinate for atom O in residue PRO:635 of segment SEG2 building segment SEG3 reading residues from pdb file myfile_frag3.pdb no residue 1 past GLU:664 of segment SEG3 Warning: add bond C(0) N(1) failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add improper failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation CA-C-N-CA failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation N-CA-C-O failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation N-CA-C-N failed in residue GLU:664 no residue 1 past ARG:549 of segment SEG4 Warning: add bond C(0) N(1) failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add improper failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation CA-C-N-CA failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation N-CA-C-O failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation N-CA-C-N failed in residue ARG:549 extracted 105 residues from pdb file generating structure at end of segment no residue 1 past ARG:549 of segment SEG4 no residue 1 before PHE:560 of segment SEG3 Warning: add bond C(0) N(1) failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add improper failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation CA-C-N-CA failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation N-CA-C-O failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation N-CA-C-N failed in residue ARG:549 Warning: add improper failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG3 Warning: add conformation C-N-CA-C failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG3 Warning: add conformation C-CA-N-HN failed in residue PHE:560 reading coordinates from pdb file myfile_frag3.pdb for segment SEG3 no residue 1 past GLU:664 of segment SEG3 Warning: add bond C(0) N(1) failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add improper failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation CA-C-N-CA failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation N-CA-C-O failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation N-CA-C-N failed in residue GLU:664 no atom O in residue GLU:664 of segment SEG3 Warning: failed to set coordinate for atom O in residue GLU:664 of segment SEG3 building segment SEG4 reading residues from pdb file myfile_frag4.pdb reading coordinates from pdb file myfile_frag3.pdb for segment SEG3 reading coordinates from pdb file myfile_frag4.pdb for segment SEG4 no atom O in residue GLU:664 of segment SEG3 Warning: failed to set coordinate for atom O in residue GLU:664 of segment SEG3 building segment SEG4 reading residues from pdb file myfile_frag4.pdb reading coordinates from pdb file myfile_frag4.pdb for segment SEG4 extracted 416 residues from pdb file generating structure at end of segment no residue 1 before HSD:134 of segment SEG4 Warning: add improper failed in residue HSD:134 no residue 1 before HSD:134 of segment SEG4 Warning: add conformation C-N-CA-C failed in residue HSD:134 no residue 1 before HSD:134 of segment SEG4 Warning: add conformation C-CA-N-HN failed in residue HSD:134 no atom O in residue ARG:549 of segment SEG4 Warning: failed to set coordinate for atom O in residue ARG:549 of segment SEG4 guessing coordinates based on topology file Warning: guessing coordinates for 4591 atoms (16 non-hydrogen) extracted 416 residues from pdb file generating structure at end of segment Warning: poorly guessed coordinates for 25 atoms (10 non-hydrogen) writing psf file new_output_psf/1i7x_psfgen_psf3.psf no residue 1 before HSD:134 of segment SEG4 Warning: add improper failed in residue HSD:134 no residue 1 before HSD:134 of segment SEG4 Warning: add conformation C-N-CA-C failed in residue HSD:134 no residue 1 before HSD:134 of segment SEG4 Warning: add conformation C-CA-N-HN failed in residue HSD:134 no atom O in residue ARG:549 of segment SEG4 Warning: failed to set coordinate for atom O in residue ARG:549 of segment SEG4 guessing coordinates based on topology file Warning: guessing coordinates for 4591 atoms (16 non-hydrogen) total of 9066 atoms total of 9133 bonds total of 16563 angles total of 24113 dihedrals total of 1606 impropers Warning: poorly guessed coordinates for 25 atoms (10 non-hydrogen) writing psf file new_output_psf/1i7x_psfgen_psf3.psf no residue 1 past ARG:549 of segment SEG4 Warning: add bond C(0) N(1) failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add improper failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation CA-C-N-CA failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation N-CA-C-O failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation N-CA-C-N failed in residue ARG:549 total of 9066 atoms total of 9133 bonds total of 16563 angles total of 24113 dihedrals total of 1606 impropers no residue 1 past ARG:549 of segment SEG4 Warning: add bond C(0) N(1) failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add improper failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation CA-C-N-CA failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation N-CA-C-O failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation N-CA-C-N failed in residue ARG:549 reading coordinates from pdb file myfile_frag4.pdb for segment SEG4 reading coordinates from pdb file myfile_frag4.pdb for segment SEG4 reading topology file parameters/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 aliasing residue HIS to HSD aliasing residue ILE atom CD1 to CD building segment SEG0 reading topology file parameters/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 reading topology file parameters/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 aliasing residue HIS to HSD aliasing residue ILE atom CD1 to CD building segment SEG0 reading topology file parameters/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 reading residues from pdb file myfile_frag0.pdb extracted 26 residues from pdb file generating structure at end of segment no residue 1 before GLU:698 of segment SEG0 Warning: add improper failed in residue GLU:698 no residue 1 before GLU:698 of segment SEG0 Warning: add conformation C-N-CA-C failed in residue GLU:698 no residue 1 before GLU:698 of segment SEG0 Warning: add conformation C-CA-N-HN failed in residue GLU:698 reading residues from pdb file myfile_frag0.pdb extracted 26 residues from pdb file generating structure at end of segment no residue 1 before GLU:698 of segment SEG0 Warning: add improper failed in residue GLU:698 no residue 1 before GLU:698 of segment SEG0 Warning: add conformation C-N-CA-C failed in residue GLU:698 no residue 1 before GLU:698 of segment SEG0 Warning: add conformation C-CA-N-HN failed in residue GLU:698 no residue 1 past GLY:723 of segment SEG0 Warning: add bond C(0) N(1) failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add improper failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation CA-C-N-CA failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation N-CA-C-O failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation N-CA-C-N failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add bond C(0) N(1) failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add improper failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation CA-C-N-CA failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation N-CA-C-O failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation N-CA-C-N failed in residue GLY:723 aliasing residue HIS to HSD aliasing residue ILE atom CD1 to CD building segment SEG0 aliasing residue HIS to HSD aliasing residue ILE atom CD1 to CD building segment SEG0 reading residues from pdb file myfile_frag0.pdb reading coordinates from pdb file myfile_frag0.pdb for segment SEG0 no atom O in residue ARG:549 of segment SEG4 Warning: failed to set coordinate for atom O in residue ARG:549 of segment SEG4 guessing coordinates based on topology file Warning: guessing coordinates for 4591 atoms (16 non-hydrogen) no atom O in residue GLY:723 of segment SEG0 Warning: failed to set coordinate for atom O in residue GLY:723 of segment SEG0 building segment SEG1 Warning: poorly guessed coordinates for 25 atoms (10 non-hydrogen) extracted 26 residues from pdb file generating structure at end of segment no residue 1 before GLU:698 of segment SEG0 Warning: add improper failed in residue GLU:698 no residue 1 before GLU:698 of segment SEG0 Warning: add conformation C-N-CA-C failed in residue GLU:698 no residue 1 before GLU:698 of segment SEG0 Warning: add conformation C-CA-N-HN failed in residue GLU:698 reading residues from pdb file myfile_frag0.pdb no residue 1 past GLY:723 of segment SEG0 Warning: add bond C(0) N(1) failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add improper failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation CA-C-N-CA failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation N-CA-C-O failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation N-CA-C-N failed in residue GLY:723 extracted 26 residues from pdb file generating structure at end of segment no residue 1 before GLU:698 of segment SEG0 Warning: add improper failed in residue GLU:698 no residue 1 before GLU:698 of segment SEG0 Warning: add conformation C-N-CA-C failed in residue GLU:698 no residue 1 before GLU:698 of segment SEG0 Warning: add conformation C-CA-N-HN failed in residue GLU:698 reading coordinates from pdb file myfile_frag0.pdb for segment SEG0 writing psf file new_output_psf/1i7x_psfgen_psf3.psf no residue 1 past GLY:723 of segment SEG0 Warning: add bond C(0) N(1) failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add improper failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation CA-C-N-CA failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation N-CA-C-O failed in residue GLY:723 no residue 1 past GLY:723 of segment SEG0 Warning: add conformation N-CA-C-N failed in residue GLY:723 no atom O in residue ARG:549 of segment SEG4 Warning: failed to set coordinate for atom O in residue ARG:549 of segment SEG4 guessing coordinates based on topology file reading coordinates from pdb file myfile_frag0.pdb for segment SEG0 reading residues from pdb file myfile_frag1.pdb Warning: guessing coordinates for 4591 atoms (16 non-hydrogen) reading coordinates from pdb file myfile_frag0.pdb for segment SEG0 no atom O in residue GLY:723 of segment SEG0 Warning: failed to set coordinate for atom O in residue GLY:723 of segment SEG0 building segment SEG1 extracted 31 residues from pdb file generating structure at end of segment no residue 1 before GLY:654 of segment SEG1 Warning: add improper failed in residue GLY:654 no residue 1 before GLY:654 of segment SEG1 Warning: add conformation C-N-CA-C failed in residue GLY:654 no residue 1 before GLY:654 of segment SEG1 Warning: add conformation C-CA-N-HN failed in residue GLY:654 no atom O in residue GLY:723 of segment SEG0 Warning: failed to set coordinate for atom O in residue GLY:723 of segment SEG0 building segment SEG1 no residue 1 past SER:684 of segment SEG1 Warning: add bond C(0) N(1) failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add improper failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation CA-C-N-CA failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation N-CA-C-O failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation N-CA-C-N failed in residue SER:684 no atom O in residue GLY:723 of segment SEG0 Warning: failed to set coordinate for atom O in residue GLY:723 of segment SEG0 building segment SEG1 Warning: poorly guessed coordinates for 25 atoms (10 non-hydrogen) writing psf file new_output_psf/1i7x_psfgen_psf3.psf total of 9066 atoms total of 9133 bonds total of 16563 angles total of 24113 dihedrals total of 1606 impropers reading residues from pdb file myfile_frag1.pdb extracted 31 residues from pdb file generating structure at end of segment no residue 1 before GLY:654 of segment SEG1 Warning: add improper failed in residue GLY:654 no residue 1 before GLY:654 of segment SEG1 Warning: add conformation C-N-CA-C failed in residue GLY:654 no residue 1 before GLY:654 of segment SEG1 Warning: add conformation C-CA-N-HN failed in residue GLY:654 reading residues from pdb file myfile_frag1.pdb extracted 31 residues from pdb file generating structure at end of segment no residue 1 before GLY:654 of segment SEG1 Warning: add improper failed in residue GLY:654 no residue 1 before GLY:654 of segment SEG1 Warning: add conformation C-N-CA-C failed in residue GLY:654 no residue 1 before GLY:654 of segment SEG1 Warning: add conformation C-CA-N-HN failed in residue GLY:654 reading coordinates from pdb file myfile_frag1.pdb for segment SEG1 no atom O in residue SER:684 of segment SEG1 Warning: failed to set coordinate for atom O in residue SER:684 of segment SEG1 building segment SEG2 reading residues from pdb file myfile_frag1.pdb extracted 31 residues from pdb file generating structure at end of segment no residue 1 past SER:684 of segment SEG1 Warning: add bond C(0) N(1) failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add improper failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation CA-C-N-CA failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation N-CA-C-O failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation N-CA-C-N failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add bond C(0) N(1) failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add improper failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation CA-C-N-CA failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation N-CA-C-O failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation N-CA-C-N failed in residue SER:684 no residue 1 before GLY:654 of segment SEG1 Warning: add improper failed in residue GLY:654 no residue 1 before GLY:654 of segment SEG1 Warning: add conformation C-N-CA-C failed in residue GLY:654 no residue 1 before GLY:654 of segment SEG1 Warning: add conformation C-CA-N-HN failed in residue GLY:654 reading residues from pdb file myfile_frag2.pdb extracted 6 residues from pdb file generating structure at end of segment no residue 1 before ARG:630 of segment SEG2 Warning: add improper failed in residue ARG:630 no residue 1 before ARG:630 of segment SEG2 Warning: add conformation C-N-CA-C failed in residue ARG:630 no residue 1 before ARG:630 of segment SEG2 Warning: add conformation C-CA-N-HN failed in residue ARG:630 no residue 1 past PRO:635 of segment SEG2 Warning: add bond C(0) N(1) failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add improper failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation CA-C-N-CA failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation N-CA-C-O failed in residue PRO:635 no residue 1 past SER:684 of segment SEG1 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation N-CA-C-N failed in residue PRO:635 Warning: add bond C(0) N(1) failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add improper failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation CA-C-N-CA failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation N-CA-C-O failed in residue SER:684 no residue 1 past SER:684 of segment SEG1 Warning: add conformation N-CA-C-N failed in residue SER:684 reading coordinates from pdb file myfile_frag1.pdb for segment SEG1 reading coordinates from pdb file myfile_frag1.pdb for segment SEG1 total of 9066 atoms reading coordinates from pdb file myfile_frag2.pdb for segment SEG2 no atom O in residue PRO:635 of segment SEG2 Warning: failed to set coordinate for atom O in residue PRO:635 of segment SEG2 building segment SEG3 no atom O in residue SER:684 of segment SEG1 Warning: failed to set coordinate for atom O in residue SER:684 of segment SEG1 building segment SEG2 total of 9133 bonds total of 16563 angles total of 24113 dihedrals total of 1606 impropers reading coordinates from pdb file myfile_frag1.pdb for segment SEG1 no atom O in residue SER:684 of segment SEG1 Warning: failed to set coordinate for atom O in residue SER:684 of segment SEG1 building segment SEG2 reading residues from pdb file myfile_frag3.pdb reading residues from pdb file myfile_frag2.pdb extracted 6 residues from pdb file generating structure at end of segment no residue 1 before ARG:630 of segment SEG2 Warning: add improper failed in residue ARG:630 no atom O in residue SER:684 of segment SEG1 Warning: failed to set coordinate for atom O in residue SER:684 of segment SEG1 building segment SEG2 no residue 1 before ARG:630 of segment SEG2 Warning: add conformation C-N-CA-C failed in residue ARG:630 no residue 1 before ARG:630 of segment SEG2 Warning: add conformation C-CA-N-HN failed in residue ARG:630 no residue 1 past PRO:635 of segment SEG2 Warning: add bond C(0) N(1) failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add improper failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation CA-C-N-CA failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation N-CA-C-O failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation N-CA-C-N failed in residue PRO:635 reading coordinates from pdb file myfile_frag2.pdb for segment SEG2 reading residues from pdb file myfile_frag2.pdb reading residues from pdb file myfile_frag2.pdb no atom O in residue PRO:635 of segment SEG2 Warning: failed to set coordinate for atom O in residue PRO:635 of segment SEG2 building segment SEG3 extracted 6 residues from pdb file generating structure at end of segment no residue 1 before ARG:630 of segment SEG2 Warning: add improper failed in residue ARG:630 no residue 1 before ARG:630 of segment SEG2 Warning: add conformation C-N-CA-C failed in residue ARG:630 no residue 1 before ARG:630 of segment SEG2 Warning: add conformation C-CA-N-HN failed in residue ARG:630 extracted 6 residues from pdb file generating structure at end of segment no residue 1 before ARG:630 of segment SEG2 Warning: add improper failed in residue ARG:630 no residue 1 before ARG:630 of segment SEG2 Warning: add conformation C-N-CA-C failed in residue ARG:630 no residue 1 before ARG:630 of segment SEG2 Warning: add conformation C-CA-N-HN failed in residue ARG:630 no residue 1 past PRO:635 of segment SEG2 Warning: add bond C(0) N(1) failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add improper failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation CA-C-N-CA failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation N-CA-C-O failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation N-CA-C-N failed in residue PRO:635 reading residues from pdb file myfile_frag3.pdb no residue 1 past PRO:635 of segment SEG2 Warning: add bond C(0) N(1) failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add improper failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation CA-C-N-CA failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation N-CA-C-O failed in residue PRO:635 no residue 1 past PRO:635 of segment SEG2 Warning: add conformation N-CA-C-N failed in residue PRO:635 extracted 105 residues from pdb file generating structure at end of segment no residue 1 before PHE:560 of segment SEG3 Warning: add improper failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG3 Warning: add conformation C-N-CA-C failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG3 Warning: add conformation C-CA-N-HN failed in residue PHE:560 reading coordinates from pdb file myfile_frag2.pdb for segment SEG2 no atom O in residue PRO:635 of segment SEG2 Warning: failed to set coordinate for atom O in residue PRO:635 of segment SEG2 building segment SEG3 reading coordinates from pdb file myfile_frag2.pdb for segment SEG2 no atom O in residue PRO:635 of segment SEG2 Warning: failed to set coordinate for atom O in residue PRO:635 of segment SEG2 building segment SEG3 extracted 105 residues from pdb file generating structure at end of segment no residue 1 before PHE:560 of segment SEG3 Warning: add improper failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG3 Warning: add conformation C-N-CA-C failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG3 Warning: add conformation C-CA-N-HN failed in residue PHE:560 no residue 1 past GLU:664 of segment SEG3 Warning: add bond C(0) N(1) failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add improper failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation CA-C-N-CA failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation N-CA-C-O failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation N-CA-C-N failed in residue GLU:664 reading residues from pdb file myfile_frag3.pdb no residue 1 past GLU:664 of segment SEG3 Warning: add bond C(0) N(1) failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add improper failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation CA-C-N-CA failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation N-CA-C-O failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation N-CA-C-N failed in residue GLU:664 extracted 105 residues from pdb file generating structure at end of segment no residue 1 before PHE:560 of segment SEG3 Warning: add improper failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG3 Warning: add conformation C-N-CA-C failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG3 Warning: add conformation C-CA-N-HN failed in residue PHE:560 reading coordinates from pdb file myfile_frag3.pdb for segment SEG3 reading residues from pdb file myfile_frag3.pdb reading coordinates from pdb file myfile_frag3.pdb for segment SEG3 no residue 1 past GLU:664 of segment SEG3 Warning: add bond C(0) N(1) failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add improper failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation CA-C-N-CA failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation N-CA-C-O failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation N-CA-C-N failed in residue GLU:664 no atom O in residue GLU:664 of segment SEG3 Warning: failed to set coordinate for atom O in residue GLU:664 of segment SEG3 building segment SEG4 extracted 105 residues from pdb file generating structure at end of segment no residue 1 before PHE:560 of segment SEG3 Warning: add improper failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG3 Warning: add conformation C-N-CA-C failed in residue PHE:560 no residue 1 before PHE:560 of segment SEG3 Warning: add conformation C-CA-N-HN failed in residue PHE:560 reading coordinates from pdb file myfile_frag3.pdb for segment SEG3 no atom O in residue GLU:664 of segment SEG3 Warning: failed to set coordinate for atom O in residue GLU:664 of segment SEG3 building segment SEG4 reading residues from pdb file myfile_frag4.pdb no atom O in residue GLU:664 of segment SEG3 Warning: failed to set coordinate for atom O in residue GLU:664 of segment SEG3 building segment SEG4 reading residues from pdb file myfile_frag4.pdb no residue 1 past GLU:664 of segment SEG3 Warning: add bond C(0) N(1) failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add improper failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation CA-C-N-CA failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation N-CA-C-O failed in residue GLU:664 no residue 1 past GLU:664 of segment SEG3 Warning: add conformation N-CA-C-N failed in residue GLU:664 reading residues from pdb file myfile_frag4.pdb extracted 416 residues from pdb file generating structure at end of segment no residue 1 before HSD:134 of segment SEG4 Warning: add improper failed in residue HSD:134 no residue 1 before HSD:134 of segment SEG4 Warning: add conformation C-N-CA-C failed in residue HSD:134 no residue 1 before HSD:134 of segment SEG4 Warning: add conformation C-CA-N-HN failed in residue HSD:134 writing pdb file new_output_psf/1i7x_psfgen_pdb3.pdb extracted 416 residues from pdb file generating structure at end of segment extracted 416 residues from pdb file generating structure at end of segment no residue 1 before HSD:134 of segment SEG4 Warning: add improper failed in residue HSD:134 no residue 1 before HSD:134 of segment SEG4 Warning: add conformation C-N-CA-C failed in residue HSD:134 no residue 1 before HSD:134 of segment SEG4 Warning: add conformation C-CA-N-HN failed in residue HSD:134 writing pdb file new_output_psf/1i7x_psfgen_pdb3.pdb no residue 1 before HSD:134 of segment SEG4 Warning: add improper failed in residue HSD:134 no residue 1 before HSD:134 of segment SEG4 Warning: add conformation C-N-CA-C failed in residue HSD:134 no residue 1 before HSD:134 of segment SEG4 Warning: add conformation C-CA-N-HN failed in residue HSD:134 reading coordinates from pdb file myfile_frag3.pdb for segment SEG3 no atom O in residue GLU:664 of segment SEG3 Warning: failed to set coordinate for atom O in residue GLU:664 of segment SEG3 building segment SEG4 no residue 1 past ARG:549 of segment SEG4 no residue 1 past ARG:549 of segment SEG4 Warning: add bond C(0) N(1) failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add improper failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation CA-C-N-CA failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation N-CA-C-O failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation N-CA-C-N failed in residue ARG:549 Warning: add bond C(0) N(1) failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add improper failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation CA-C-N-CA failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation N-CA-C-O failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation N-CA-C-N failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add bond C(0) N(1) failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add improper failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation CA-C-N-CA failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation N-CA-C-O failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation N-CA-C-N failed in residue ARG:549 reading residues from pdb file myfile_frag4.pdb reading coordinates from pdb file myfile_frag4.pdb for segment SEG4 reading coordinates from pdb file myfile_frag4.pdb for segment SEG4 reading coordinates from pdb file myfile_frag4.pdb for segment SEG4 no atom O in residue ARG:549 of segment SEG4 Warning: failed to set coordinate for atom O in residue ARG:549 of segment SEG4 guessing coordinates based on topology file Warning: guessing coordinates for 4591 atoms (16 non-hydrogen) no atom O in residue ARG:549 of segment SEG4 Warning: failed to set coordinate for atom O in residue ARG:549 of segment SEG4 guessing coordinates based on topology file Warning: guessing coordinates for 4591 atoms (16 non-hydrogen) Warning: poorly guessed coordinates for 25 atoms (10 non-hydrogen) extracted 416 residues from pdb file generating structure at end of segment no residue 1 before HSD:134 of segment SEG4 Warning: add improper failed in residue HSD:134 no residue 1 before HSD:134 of segment SEG4 Warning: add conformation C-N-CA-C failed in residue HSD:134 no residue 1 before HSD:134 of segment SEG4 Warning: add conformation C-CA-N-HN failed in residue HSD:134 writing pdb file new_output_psf/1i7x_psfgen_pdb3.pdb writing pdb file new_output_psf/1i7x_psfgen_pdb3.pdb Warning: poorly guessed coordinates for 25 atoms (10 non-hydrogen) no atom O in residue ARG:549 of segment SEG4 Warning: failed to set coordinate for atom O in residue ARG:549 of segment SEG4 guessing coordinates based on topology file Warning: guessing coordinates for 4591 atoms (16 non-hydrogen) Warning: poorly guessed coordinates for 25 atoms (10 non-hydrogen) writing psf file new_output_psf/1i7x_psfgen_psf3.psf no residue 1 past ARG:549 of segment SEG4 Warning: add bond C(0) N(1) failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add improper failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation CA-C-N-CA failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation N-CA-C-O failed in residue ARG:549 no residue 1 past ARG:549 of segment SEG4 Warning: add conformation N-CA-C-N failed in residue ARG:549 total of 9066 atoms total of 9133 bonds total of 16563 angles total of 24113 dihedrals total of 1606 impropers writing psf file new_output_psf/1i7x_psfgen_psf3.psf writing psf file new_output_psf/1i7x_psfgen_psf3.psf PSFGEN from NAMD 2.5b1 for Linux-Alpha PSFGEN from NAMD 2.5b1 for Linux-Alpha total of 9066 atoms total of 9133 bonds total of 16563 angles total of 24113 dihedrals total of 1606 impropers total of 9066 atoms total of 9133 bonds total of 16563 angles total of 24113 dihedrals total of 1606 impropers reading coordinates from pdb file myfile_frag4.pdb for segment SEG4 no atom O in residue ARG:549 of segment SEG4 Warning: failed to set coordinate for atom O in residue ARG:549 of segment SEG4 guessing coordinates based on topology file Warning: guessing coordinates for 4591 atoms (16 non-hydrogen) Warning: poorly guessed coordinates for 25 atoms (10 non-hydrogen) writing psf file new_output_psf/1i7x_psfgen_psf3.psf PSFGEN from NAMD 2.5b1 for Linux-Alpha PSFGEN from NAMD 2.5b1 for Linux-Alpha total of 9066 atoms total of 9133 bonds total of 16563 angles total of 24113 dihedrals total of 1606 impropers writing pdb file new_output_psf/1i7x_psfgen_pdb3.pdb writing pdb file new_output_psf/1i7x_psfgen_pdb3.pdb writing pdb file new_output_psf/1i7x_psfgen_pdb3.pdb PSFGEN from NAMD 2.5b1 for Linux-Alpha PSFGEN from NAMD 2.5b1 for Linux-Alpha PSFGEN from NAMD 2.5b1 for Linux-Alpha writing pdb file new_output_psf/1i7x_psfgen_pdb3.pdb PSFGEN from NAMD 2.5b1 for Linux-Alpha