[gmx-users] g_sdf

Dallas B. Warren Dallas.Warren at pharm.monash.edu.au
Wed Apr 8 01:41:44 CEST 2009

What exactly your issue with using g_sdf?

You need to supple a trajectory, index, and topology.  Index contains
the three reference atoms for the molecule, plus the atom you are
calculating the sdf to.  Selection of the correct grid size and binwidth
is required to get something that looks as you want it.

Catch ya,

Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

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