Info) VMD for LINUXAMD64, version 1.9.3 (November 30, 2016) Info) http://www.ks.uiuc.edu/Research/vmd/ Info) Email questions and bug reports to vmd@ks.uiuc.edu Info) Please include this reference in published work using VMD: Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38. Info) ------------------------------------------------------------- Info) Multithreading available, 8 CPUs detected. Info) CPU features: SSE2 AVX AVX2 FMA Info) Free system memory: 3568MB (45%) ERROR) -dispdev options are 'win' 'opengl' (default), 'openglpbuffer', 'cave', 'caveforms', 'freevr', 'freevrforms', or 'text | none' Info) No CUDA accelerator devices available. Warning) Detected X11 'Composite' extension: if incorrect display occurs Warning) try disabling this X server option. Most OpenGL drivers Warning) disable stereoscopic display when 'Composite' is enabled. Info) OpenGL renderer: Gallium 0.4 on NV117 Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFS) Info) Full GLSL rendering mode is available. Info) Textures: 2-D (16384x16384), 3-D (512x512x512), Multitexture (8) Info) Dynamically loaded 2 plugins in directory: Info) /home/natasha/Downloads/bin/lib_vmd_1.9.3/vmd/plugins/LINUXAMD64/molfile invalid command name "psf/pdb" Info) Using plugin pdb for structure file bnm170-rscb.pdb Info) Using plugin pdb for coordinates from file bnm170-rscb.pdb Info) Determining bond structure from distance search ... Info) Eliminating bonds duplicated from existing structure... Info) Analyzing structure ... Info) Atoms: 31 Info) Bonds: 33 Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0 Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0 Info) Residues: 1 Info) Waters: 0 Info) Segments: 1 Info) Fragments: 1 Protein: 0 Nucleic: 0 Info) Finished with coordinate file bnm170-rscb.pdb. 0 atomselect0 Info) Opened coordinate file A.pdb for writing. Info) Finished with coordinate file A.pdb. 1.6.4 psfgen) reading topology file top_all22_prot.rtf psfgen) >>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<< psfgen) >>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<< psfgen) >>>>>>>>>>>>>>>>>>>>>> December, 2003 <<<<<<<<<<<<<<<<<<<<<<<<<< psfgen) All comments to ADM jr. via the CHARMM web site: www.charmm.org psfgen) parameter set discussion forum psfgen) psfgen) Created by CHARMM version 31 1 psfgen) cross-term entries present in topology definitions psfgen) reading topology file top_all36_cgenff.rtf psfgen) -------------------------------------------------------------------------- * psfgen) CGenFF: Topology for the Charmm General Force Field v. 2b8 * psfgen) for Small Molecule Drug Design * psfgen) -------------------------------------------------------------------------- * psfgen) psfgen) Created by CHARMM version 36 1 psfgen) reading topology file bnm170-post.str psfgen) Toppar stream file generated by psfgen) CHARMM General Force Field (CGenFF) program version 1.0.0 psfgen) For use with CGenFF version 3.0.1 psfgen) psfgen) reading topology from stream file psfgen) Topologies generated by psfgen) CHARMM General Force Field (CGenFF) program version 1.0.0 psfgen) psfgen) Created by CHARMM version 36 1 psfgen) skipping parameters in stream file psfgen) Parameters generated by analogy by psfgen) CHARMM General Force Field (CGenFF) program version 1.0.0 psfgen) psfgen) aliasing residue HIS to HSE psfgen) aliasing residue ILE atom CD1 to CD psfgen) aliasing residue 1C1 to D121 psfgen) aliasing residue 5VG atom N01 to N1 psfgen) aliasing residue 5VG atom C02 to C2 psfgen) aliasing residue 5VG atom N03 to N3 psfgen) aliasing residue 5VG atom C04 to C4 psfgen) aliasing residue 5VG atom C05 to C5 psfgen) aliasing residue 5VG atom C06 to C6 psfgen) aliasing residue 5VG atom C07 to C7 psfgen) aliasing residue 5VG atom C08 to C8 psfgen) aliasing residue 5VG atom C09 to C9 psfgen) aliasing residue 5VG atom CL1 to Cl25 psfgen) building segment A psfgen) reading residues from pdb file A.pdb psfgen) extracted 1 residues from pdb file psfgen) Info: generating structure...segment complete. psfgen) reading coordinates from pdb file A.pdb for segment A psfgen) Warning: failed to set coordinate for atom N 5VG:501 A psfgen) Warning: failed to set coordinate for atom C 5VG:501 A psfgen) Warning: failed to set coordinate for atom C00 5VG:501 A psfgen) Warning: failed to set coordinate for atom CL25 5VG:501 A psfgen) Warning: failed to set coordinate for atom C02 5VG:501 A psfgen) Warning: failed to set coordinate for atom C04 5VG:501 A psfgen) Warning: failed to set coordinate for atom C05 5VG:501 A psfgen) Warning: failed to set coordinate for atom C06 5VG:501 A psfgen) Warning: failed to set coordinate for atom N14 5VG:501 A psfgen) Warning: failed to set coordinate for atom O16 5VG:501 A psfgen) Warning: failed to set coordinate for atom O18 5VG:501 A psfgen) Warning: failed to set coordinate for atom N19 5VG:501 A psfgen) Warning: failed to set coordinate for atom N28 5VG:501 A psfgen) Warning: failed to set coordinate for atom F23 5VG:501 A psfgen) Info: guessing coordinates for 40 atoms (14 non-hydrogen) psfgen) Warning: poorly guessed coordinates for 40 atoms (14 non-hydrogen): psfgen) Warning: poorly guessed coordinate for atom N2 5VG:501 A psfgen) Warning: poorly guessed coordinate for atom N4 5VG:501 A psfgen) Warning: poorly guessed coordinate for atom N5 5VG:501 A psfgen) Warning: poorly guessed coordinate for atom N6 5VG:501 A psfgen) Warning: poorly guessed coordinate for atom C14 5VG:501 A psfgen) Warning: poorly guessed coordinate for atom C16 5VG:501 A psfgen) Warning: poorly guessed coordinate for atom C18 5VG:501 A psfgen) Warning: poorly guessed coordinate for atom C19 5VG:501 A psfgen) Warning: poorly guessed coordinate for atom C23 5VG:501 A psfgen) Warning: poorly guessed coordinate for atom C25 5VG:501 A psfgen) Warning: poorly guessed coordinate for atom O28 5VG:501 A psfgen) Warning: poorly guessed coordinate for atom O29 5VG:501 A psfgen) Warning: poorly guessed coordinate for atom CL30 5VG:501 A psfgen) Warning: poorly guessed coordinate for atom F31 5VG:501 A psfgen) Warning: poorly guessed coordinate for atom H32 5VG:501 A psfgen) Warning: poorly guessed coordinate for atom H33 5VG:501 A psfgen) Warning: poorly guessed coordinate for atom H34 5VG:501 A psfgen) Warning: poorly guessed coordinate for atom H35 5VG:501 A psfgen) Warning: poorly guessed coordinate for atom H36 5VG:501 A psfgen) Warning: poorly guessed coordinate for atom H37 5VG:501 A psfgen) Warning: poorly guessed coordinate for atom H38 5VG:501 A psfgen) Warning: poorly guessed coordinate for atom H39 5VG:501 A psfgen) Warning: poorly guessed coordinate for atom H40 5VG:501 A psfgen) Warning: poorly guessed coordinate for atom H41 5VG:501 A psfgen) Warning: poorly guessed coordinate for atom H42 5VG:501 A psfgen) Warning: poorly guessed coordinate for atom H43 5VG:501 A psfgen) Warning: poorly guessed coordinate for atom H44 5VG:501 A psfgen) Warning: poorly guessed coordinate for atom H45 5VG:501 A psfgen) Warning: poorly guessed coordinate for atom H46 5VG:501 A psfgen) Warning: poorly guessed coordinate for atom H47 5VG:501 A psfgen) Warning: poorly guessed coordinate for atom H48 5VG:501 A psfgen) Warning: poorly guessed coordinate for atom H49 5VG:501 A psfgen) Warning: poorly guessed coordinate for atom H50 5VG:501 A psfgen) Warning: poorly guessed coordinate for atom H51 5VG:501 A psfgen) Warning: poorly guessed coordinate for atom H52 5VG:501 A psfgen) Warning: poorly guessed coordinate for atom H53 5VG:501 A psfgen) Warning: poorly guessed coordinate for atom H54 5VG:501 A psfgen) Warning: poorly guessed coordinate for atom H55 5VG:501 A psfgen) Warning: poorly guessed coordinate for atom H56 5VG:501 A psfgen) Warning: poorly guessed coordinate for atom H57 5VG:501 A psfgen) Info: writing psf file bnm170.psf psfgen) total of 57 atoms psfgen) total of 59 bonds psfgen) total of 102 angles psfgen) total of 151 dihedrals psfgen) total of 3 impropers psfgen) total of 0 explicit exclusions psfgen) Structure requires EXTended PSF format psfgen) total of 0 cross-terms psfgen) Info: psf file complete. psfgen) Info: writing pdb file bnm170.pdb psfgen) Info: Atoms with guessed coordinates will have occupancy of 0.0. psfgen) Info: pdb file complete. psfplugin) Detected a Charmm PSF EXTEnded file Info) Using plugin psf for structure file bnm170.psf psfplugin) no cross-terms defined in PSF file. Info) Analyzing structure ... Info) Atoms: 57 Info) Bonds: 59 Info) Angles: 102 Dihedrals: 151 Impropers: 3 Cross-terms: 0 Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0 Info) Residues: 1 Info) Waters: 0 Info) Segments: 1 Info) Fragments: 1 Protein: 0 Nucleic: 0 1 Info) Using plugin pdb for coordinates from file bnm170.pdb Info) Finished with coordinate file bnm170.pdb. 1 atomselect1 Info) Opened coordinate file bnm170_shift.pdb for writing. Info) Finished with coordinate file bnm170_shift.pdb. {-3.956636428833008 -7.422379016876221 -3.1767139434814453} {4.444362640380859 6.305621147155762 4.062284469604492} -3.956636428833008 -7.422379016876221 -3.1767139434814453 4.444362640380859 6.305621147155762 4.062284469604492 10 10 10 14.44436264038086 16.30562114715576 14.062284469604492 -13.956636428833008 -17.42237901687622 -13.176713943481445 28.400999069213867 33.72800016403198 27.238998413085938 file16 can't read "bo": no such variable 1.7 Info) generating solute plus one replica of water... psfgen) reading structure from psf file bnm170.psf psfgen) psf file does not contain cross-terms psfgen) reading coordinates from pdb file bnm170_shift.pdb psfgen) reading structure from psf file /home/natasha/Downloads/bin/lib_vmd_1.9.3/vmd/plugins/noarch/tcl/solvate1.7/wat.psf psfgen) psf file does not contain cross-terms psfgen) reading coordinates from pdb file /home/natasha/Downloads/bin/lib_vmd_1.9.3/vmd/plugins/noarch/tcl/solvate1.7/wat.pdb psfgen) Info: writing psf file combine.psf psfgen) total of 27840 atoms psfgen) total of 18581 bonds psfgen) total of 18624 angles psfgen) total of 151 dihedrals psfgen) total of 3 impropers psfgen) total of 0 explicit exclusions psfgen) Structure requires EXTended PSF format psfgen) total of 0 cross-terms psfgen) Info: psf file complete. psfgen) Info: writing pdb file combine.pdb psfgen) Info: pdb file complete. psfplugin) Detected a Charmm PSF EXTEnded file Info) Using plugin psf for structure file combine.psf psfplugin) no cross-terms defined in PSF file. Info) Analyzing structure ... Info) Atoms: 27840 Info) Bonds: 18581 Info) Angles: 18624 Dihedrals: 151 Impropers: 3 Cross-terms: 0 Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0 Info) Residues: 9262 Info) Waters: 9261 Info) Segments: 2 Info) Fragments: 9262 Protein: 0 Nucleic: 0 Info) Using plugin pdb for coordinates from file combine.pdb Info) Finished with coordinate file combine.pdb. Info) generating water residue lists... Info) single water residue type, creating residue list... Info) replicating 1 water segments, 1 by 1 by 1 psfgen) reading topology file /home/natasha/Downloads/bin/lib_vmd_1.9.3/vmd/plugins/noarch/tcl/solvate1.7/wat.top psfgen) >>>>>> Combined CHARMM All-Hydrogen Topology File for <<<<<<<<< psfgen) >>>>>>>>> CHARMM22 Proteins and CHARMM27 Lipids <<<<<<<<<< psfgen) from psfgen) >>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<< psfgen) >>>>>>>>>>>>>>>>>>>>> August 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<<< psfgen) >>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<< psfgen) >>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<< psfgen) and psfgen) \\\\\\\ CHARMM27 All-Hydrogen Lipid Topology File /////// psfgen) \\\\\\\\\\\\\\\\\\ Developmental ///////////////////////// psfgen) Alexander D. MacKerell Jr. psfgen) August 1999 psfgen) All comments to ADM jr. email: alex,mmiris.ab.umd.edu psfgen) telephone: 410-706-7442 psfgen) psfgen) Created by CHARMM version 27 1 psfgen) building segment WT1 psfgen) setting patch for first residue to NONE psfgen) setting patch for last residue to NONE psfgen) Info: generating structure...segment complete. psfgen) Info: writing psf file bnm170_wb1.psf psfgen) total of 2310 atoms psfgen) total of 1561 bonds psfgen) total of 853 angles psfgen) total of 151 dihedrals psfgen) total of 3 impropers psfgen) total of 0 explicit exclusions psfgen) Structure requires EXTended PSF format psfgen) total of 0 cross-terms psfgen) Info: psf file complete. psfgen) Info: writing pdb file bnm170_wb1.pdb psfgen) Info: pdb file complete. psfgen) clearing structure, preserving topology and aliases psfplugin) Detected a Charmm PSF EXTEnded file Info) Using plugin psf for structure file bnm170_wb1.psf psfplugin) no cross-terms defined in PSF file. Info) Analyzing structure ... Info) Atoms: 2310 Info) Bonds: 1561 Info) Angles: 853 Dihedrals: 151 Impropers: 3 Cross-terms: 0 Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0 Info) Residues: 752 Info) Waters: 751 Info) Segments: 2 Info) Fragments: 752 Protein: 0 Nucleic: 0 Info) Using plugin pdb for coordinates from file bnm170_wb1.pdb Info) Finished with coordinate file bnm170_wb1.pdb. Info) Opened coordinate file bnm170_wb1.pdb for writing. Info) Finished with coordinate file bnm170_wb1.pdb. Info) Extra structure overlap safety check... Info) Solvate completed successfully. 1.4 Autoionize) Reading bnm170_wb1.psf/bnm170_wb1.pdb... psfgen) clearing structure, preserving topology and aliases psfgen) reading structure from psf file bnm170_wb1.psf psfgen) psf file does not contain cross-terms psfgen) reading coordinates from pdb file bnm170_wb1.pdb psfplugin) Detected a Charmm PSF EXTEnded file Info) Using plugin psf for structure file bnm170_wb1.psf psfplugin) no cross-terms defined in PSF file. Info) Analyzing structure ... Info) Atoms: 2310 Info) Bonds: 1561 Info) Angles: 853 Dihedrals: 151 Impropers: 3 Cross-terms: 0 Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0 Info) Residues: 752 Info) Waters: 751 Info) Segments: 2 Info) Fragments: 752 Protein: 0 Nucleic: 0 Info) Using plugin pdb for coordinates from file bnm170_wb1.pdb Info) Finished with coordinate file bnm170_wb1.pdb. Autoionize) System net charge before adding ions: 2.0000001250300556e. Autoionize) Number of ions required for neutralizing the system: 0 SOD and 2 CLA. Autoionize) Ions to be placed: Autoionize) 2 CLA Autoionize) Required min distance from molecule: 5A. Autoionize) Required min distance between ions: 5A. Autoionize) Output file prefix 'bnm170_wb'. Autoionize) Ions will be added to segname ION. Autoionize) Obtained positions for 2 ions. Autoionize) Tagged 2 water molecules for deletion. Autoionize) Deleted 2 water molecules. Autoionize) Reading CHARMM topology file... psfgen) reading topology file /home/natasha/Downloads/bin/lib_vmd_1.9.3/vmd/plugins/noarch/tcl/readcharmmtop1.2/toppar_water_ions_namd.str psfgen) Toplogy and parameter information for water and ions. psfgen) psfgen) reading topology from stream file psfgen) Topology for water and ions psfgen) psfgen) Created by CHARMM version 31 1 psfgen) skipping parameters in stream file psfgen) Parameters for water and ions psfgen) psfgen) skipping parameters in stream file psfgen) NBFix between carboxylate and sodium psfgen) psfgen) building segment ION psfgen) setting patch for first residue to NONE psfgen) setting patch for last residue to NONE psfgen) Info: generating structure...segment complete. Autoionize) Randomizing ion positions... Autoionize) Assigning ion coordinates... psfgen) Info: writing psf file bnm170_wb.psf psfgen) total of 2306 atoms psfgen) total of 1557 bonds psfgen) total of 851 angles psfgen) total of 151 dihedrals psfgen) total of 3 impropers psfgen) total of 0 explicit exclusions psfgen) Structure requires EXTended PSF format psfgen) total of 0 cross-terms psfgen) Info: psf file complete. psfgen) Info: writing pdb file bnm170_wb.pdb psfgen) Info: pdb file complete. Autoionize) Loading new system with added ions... psfplugin) Detected a Charmm PSF EXTEnded file Info) Using plugin psf for structure file bnm170_wb.psf psfplugin) no cross-terms defined in PSF file. Info) Analyzing structure ... Info) Atoms: 2306 Info) Bonds: 1557 Info) Angles: 851 Dihedrals: 151 Impropers: 3 Cross-terms: 0 Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0 Info) Residues: 752 Info) Waters: 749 Info) Segments: 3 Info) Fragments: 752 Protein: 0 Nucleic: 0 Info) Using plugin pdb for coordinates from file bnm170_wb.pdb Info) Finished with coordinate file bnm170_wb.pdb. Info) Opened coordinate file bnm170_wb.pdb for writing. Info) Finished with coordinate file bnm170_wb.pdb. Autoionize) System net charge after adding ions: 1.25030055642128e-7e. Autoionize) All done. Info) VMD for LINUXAMD64, version 1.9.3 (November 30, 2016) Info) Exiting normally. vmd >