[gmx-users] top file confusion

Dallas B. Warren Dallas.Warren at vcp.monash.edu.au
Fri Feb 10 05:37:26 CET 2006

> 	      the gromacs3.3 has an decane.itp file included in 
> top folder, but the decane top i generated with pdb2gmx has 
> somthing different. the function type of dihedrals for the 
> former is 3 while the latter is 1, i don't know what a 3 type 
> is for dihedrals. is it a mistake for the itp file enclosed?

Check chapter 5, the section on topology files.  It tells you what each
number stands for, then you can go back to the earlier chapters and get
full details.

In this case 1 = proper dihedral, 3 = Ryckaert-Bellemans dihedral.

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 9073
When the only tool you own is a hammer, every problem begins to resemble
a nail.

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