Dear Dr Kohlmeyer,
This is what I when I type the command:
:~/Desktop$ vmd -dispdev text -e simplexyztodata.tcl
rlwrap: Command not found.
Info) VMD for LINUX, version 1.8.7 (August 1, 2009)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to [email protected]...
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) Free system memory: 7764MB (96%)
Info) No CUDA accelerator devices available.
can't find package topotools 1.1
2.5
Info) Using plugin xyz for structure file chain.xyz
Info) Using plugin xyz for coordinates from file chain.xyz
Info) Finished with coordinate file chain.xyz.
Info) Analyzing structure ...
Info) Atoms: 11
Info) Bonds: 0
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 11
Info) Waters: 0
Info) Segments: 1
Info) Fragments: 11 Protein: 0 Nucleic: 0
0
atomselect0
Info) Determining bond structure from distance search ...
Info) Bond count: 10
invalid command name "topo"
Info) Analyzing structure ...
Info) Atoms: 11
Info) Bonds: 10
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
invalid command name "topo"
Info) VMD for LINUX, version 1.8.7 (August 1, 2009)
Info) Exiting normally.
and this when I do the following:
:~/Desktop$ vmd -dispdev text -e twochainsfromone.tcl
rlwrap: Command not found.
Info) VMD for LINUX, version 1.8.7 (August 1, 2009)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to [email protected]...
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) Free system memory: 7758MB (96%)
Info) No CUDA accelerator devices available.
can't find package topotools 1.1
2.5
Info) Using plugin xyz for structure file chain.xyz
Info) Using plugin xyz for coordinates from file chain.xyz
Info) Finished with coordinate file chain.xyz.
Info) Analyzing structure ...
Info) Atoms: 11
Info) Bonds: 0
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 11
Info) Waters: 0
Info) Segments: 1
Info) Fragments: 11 Protein: 0 Nucleic: 0
0
atomselect0
11
22
1
atomselect1
name type radius resname mass x y z
{A A 0.8500000238418579 CHA 1.0 0.0 0.0 -5.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 -4.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 -3.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 -2.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 -1.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 0.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 1.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 2.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 3.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 4.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 5.0}
{A A 0.8500000238418579 CHA 1.0 0.0 0.0 -20.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 -19.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 -18.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 -17.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 -16.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 -15.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 -14.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 -13.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 -12.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 -11.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 -10.0}
{A A 0.8500000238418579 CHA 1.0 0.0 0.0 -5.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 -4.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 -3.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 -2.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 -1.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 0.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 1.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 2.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 3.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 4.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 5.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 -20.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 -19.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 -18.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 -17.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 -16.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 -15.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 -14.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 -13.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 -12.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 -11.0} {A A 0.8500000238418579 CHA 1.0 0.0 0.0 -10.0}
Info) Determining bond structure from distance search ...
Info) Bond count: 20
invalid command name "topo"
Info) Analyzing structure ...
Info) Atoms: 22
Info) Bonds: 20
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 2
Info) Waters: 0
Info) Segments: 1
Info) Fragments: 2 Protein: 0 Nucleic: 0
invalid command name "topo"
psfplugin) WARNING: PSF file is incomplete, no angles, dihedrals,
psfplugin) impropers, or cross-terms will be written.
Info) Opened coordinate file twochains.psf for writing.
Info) Finished with coordinate file twochains.psf.
1
Info) VMD for LINUX, version 1.8.7 (August 1, 2009)
Info) Exiting normally.