[gmx-users] pdb2gmx: Amber trajectory conversion

Dallas B. Warren Dallas.Warren at vcp.monash.edu.au
Wed Jul 19 02:21:06 CEST 2006

The script that deals with converting trajectories is trjconv.  Have a
look at the documentation, that will show you the formats it can handle,
no idea what Amber format is, but as long as you can get it into one of
the ones it can use should be fine.  Plus, with g_cluster I suspect you
will require a topology file to be able to do the analysis, which will
be your major sticking point.

Note that pdb2gmx converts pdb coordinate files to generate a topology
file (and the residues/molecules have to be known by the database
otherwise you have to make by hand etc).

Catch ya,

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 9524
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

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