Difference between revisions of "VMD"
From Rizzo_Lab
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| + | ==Installation== | ||
[[Installing MSMS for VMD]] | [[Installing MSMS for VMD]] | ||
| + | vmd sets LD_LIBRARY_PATH itself. If there is a problem with wrong versions of shared libraries, copy them into the vmd lib directory, and vmd will find them. | ||
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| + | ==Running vmd== | ||
A great resource is the user manual [http://www.ks.uiuc.edu/Research/vmd/current/ug.pdf]. | A great resource is the user manual [http://www.ks.uiuc.edu/Research/vmd/current/ug.pdf]. | ||
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To run a script (in windows) type source in the command line followed by the fill name. | To run a script (in windows) type source in the command line followed by the fill name. | ||
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Useful atom selection commands: | Useful atom selection commands: | ||
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same resid as within 5 of resname LIG | same resid as within 5 of resname LIG | ||
| + | == Example Scripts for VMD == | ||
here is a script to calculate rmsd's: [[vmd.rmsd.csh]]. | here is a script to calculate rmsd's: [[vmd.rmsd.csh]]. | ||
Latest revision as of 07:41, 5 May 2011
Installation
vmd sets LD_LIBRARY_PATH itself. If there is a problem with wrong versions of shared libraries, copy them into the vmd lib directory, and vmd will find them.
Running vmd
A great resource is the user manual [1].
One can run scripts in VMD command line (example scripts).
To run a script (in windows) type source in the command line followed by the fill name.
Useful atom selection commands:
"within <distance> of <selection>" "same <property> as <selection>" same resid as within 5 of resname LIG
Example Scripts for VMD
here is a script to calculate rmsd's: vmd.rmsd.csh.
