Simulaid tutorial

Simulaid examples

For each function described here the following information is given here:

The screenshot of the run. Answers the user typed or selected as default are shown in bold face.
An input file xxx.inp that can be used to rerun this job as
simulaid < xxx.inp.
These files were produced by instructing each run to produce a log of the answers used.
If applicable, the output (ASCI text) file describing the various calculated properties
If applicable, a (Postscript) plot file describing the results.
Adobe Acrobat can distill Postcript files into pdf format. Also, GSview is a free Postscript viewer.

Note, that the list of all the menu options can be obtained from the startup screen by typing f.

DSSP:	Screen shot	Input file to rerun	Output file	Output plot
Hydrogen bond:	Screen shot	Input file to rerun	Output file	Output plot
2D RMSD map:	Screen shot	Input file to rerun	Output file	Output plot
Helix analyses:	Screen shot	Input file to rerun	Output file	Output plot
Radius of gyration:	Screen shot	Input file to rerun	Output file	Output plot
Orientation optimization:	Screen shot	Input file to rerun	Optimized file
Orient to a bond:	Screen shot	Input file to rerun	Oriented file
Extracting sequence:	Screen shot	Input file to rerun	Sequence file
File format conversion:	Screen shot	Input file to rerun	Converted file
Trajectory conversion:	Screen shot	Input file to rerun
Test system starting structure (PDB)
Test system starting structure (Schroedinger Maestro)
Test system MD trajectory in Charmm format (Intel binary)
Test system MD trajectory in Amber format (ASCI text)
Simulaid version with these examples			Source code	Executable