[gmx-users] kindly guide me!
Dallas B. Warren
Dallas.Warren at vcp.monash.edu.au
Wed Jun 1 00:41:48 CEST 2005
> Let me know how to make use of the VMD to view the gromacs file of
the drug-enzyme complex?
Start up VMD, click on "File", "New Molecule", "Browse", find the
molecule file (*.gro) and "Load" it.
> Is it possible to visualize the same in the INSIGHT II before
entering into simulation or solvation step?
? Not sure what you are asking there. Depends on what file formats you
can load into Insight, if it can handle the *.gro file, then you can
load and view it.
> What is the desired command to be given to see the drug-enzyme
complex with hydrogens added in gromacs?
Just load it up and all atoms present in the *.gro file will be shown.
Then change the representation to suit.
> How to get the VMD software?
Type "VMD" into google.com, or any other search engine, find the VMD
home page and get it from there.
>Is there any other molecular visualisation tool for viewing the
There are plenty, few have been mentioned on this emailing list, so try
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9073
When the only tool you own is a hammer, every problem begins to resemble
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