Instructions to run Sparky in Mac OSX
Step 1 - Run dmg file, which also opens the terminal from X11.
Step 2 - Open Finder, Open Sparky 3.115, Right click on Sparky icon and click on “Show Package Contents”
Step 3 - Go to Contents/Resources/bin, click on any file to get the path
Step 4 - Take the path in X11 terminal to reach there and execute file by “./filename” e.g.
./vnmr2ucsf /Users/Chemist/Desktop/procpar
/Users/Chemist/Desktop/phasefile
/Users/Chemist/Desktop/filename.ucsf H H
Step 5 - filename.ucsf can be opened using sparky. Methods for Processing/Integrating/Labelling is documented in manual
CONTENTS
1. Tricks in organic reactions
2. Instructions to run Sparky in Mac OSX
3. Instructions to run NMRpipe in Mac OSX
4. Gaussian Troubleshooting: Identical Atom Ordering
2. Instructions to run Sparky in Mac OSX
3. Instructions to run NMRpipe in Mac OSX
4. Gaussian Troubleshooting: Identical Atom Ordering
Thursday, December 30, 2010
Instructions to run NMRpipe in Mac OSX
Step 1 - Open terminal through X11.
Step 2 - Enter: tcsh (to move from bash shell to c shell)
Step 3 - Go to the directory cd Documents/NMRpipe
Step 4 - Then, enter: source com/nmrInit.mac.com
Step 5 - Then, enter: source dynamo/com/dynInit.com
Step 6 - Then, enter: source com/font.com
Step 7 - Then, enter: setenv NMR_CONT CORRECT_ALL (to override expiration date)
Step 8 - Then, enter: nmrDraw (to open graphics panel)
Step 1 - Open terminal through X11.
Step 2 - Enter: tcsh (to move from bash shell to c shell)
Step 3 - Go to the directory cd Documents/NMRpipe
Step 4 - Then, enter: source com/nmrInit.mac.com
Step 5 - Then, enter: source dynamo/com/dynInit.com
Step 6 - Then, enter: source com/font.com
Step 7 - Then, enter: setenv NMR_CONT CORRECT_ALL (to override expiration date)
Step 8 - Then, enter: nmrDraw (to open graphics panel)
Gaussian Troubleshooting
Location Transition States: Identical Atom Ordering for QST2 or QST3 jobs
Step 1 - Open a new "Molecule Group" in Gaussview
Step 2 - Draw the reactant molecules
Step 3 - Click "Edit" and then "Copy"
Step 4 - Click "Edit" and then "Paste" and select "Add to Molecule Group"
Checkpoint: Click "View" and select "Labels" to confirm order of atoms
Step 5 - Click "View Both" in toolbar, modify the structures
Checkpoint: Optimize individual structure separately and cut-paste to the molecule group replacing the unoptimized structure
Step 6 - Submit QST2 job or repeat from Step 3 for QST3
Checkpoint: For submitting job, click "Calculate", select "Job Type", select "Optimization" and set "Optimization to a" - TS(QST2) or TS(QST3)
Location Transition States: Identical Atom Ordering for QST2 or QST3 jobs
Step 1 - Open a new "Molecule Group" in Gaussview
Step 2 - Draw the reactant molecules
Step 3 - Click "Edit" and then "Copy"
Step 4 - Click "Edit" and then "Paste" and select "Add to Molecule Group"
Checkpoint: Click "View" and select "Labels" to confirm order of atoms
Step 5 - Click "View Both" in toolbar, modify the structures
Checkpoint: Optimize individual structure separately and cut-paste to the molecule group replacing the unoptimized structure
Step 6 - Submit QST2 job or repeat from Step 3 for QST3
Checkpoint: For submitting job, click "Calculate", select "Job Type", select "Optimization" and set "Optimization to a" - TS(QST2) or TS(QST3)
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