[gmx-users] kindly guide me!

[Dallas B. Warren]

 > 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
molecule? 
 
There are plenty, few have been mentioned on this emailing list, so try
a search.
 
Catch ya,
Dr. Dallas Warren
Lecturer
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
a nail. 

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