The VMD interface consists of 3 windows
VMD Main – Main area with options to load molecules, change
display options, and various analysis options
VMD OpenGL Display – The display window, you should see VMD
spinning in red, green and blue.
A Terminal Window – displays the logfile, accepts commands
Loading a Molecule
On the VMD Main window, select “File” -> “New Molecule”
This brings up a new window called the Molecule File Browser, click on “Browse”, and browse to your TOPLOGY file, it will normally end in .prmtop. The filetype will be automatically recognized as AMBER7 Parm. Click on “Load”.
The terminal window should give some output like this:
Info) Analyzing structure ...
Info) Atoms: 510
Info) Bonds: 532
Info) Angles: 0
Dihedrals: 0 Impropers:
0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0
Dihedraltypes: 0
Impropertypes: 0
Info) Residues: 26
Info) Waters: 0
Info) Segments: 1
Info) Fragments: 2 Protein: 0
Nucleic: 0
Go back to
the Molecule File Browser and click “Browse”, then select your trajectory file,
this should end in .mdcrd. VMD will automatically select “AMBER coordinates”
because of the MDCRD file extension. This will be fine if you used the “nobox”
command in ptraj. But if you have a periodic box, then you should change this
option to “AMBER coordinates with periodic box”
Only use the periodic box if your trajectory file defines this
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