[gmx-users] pdb2gmx Problems

Dallas Warren dallas.warren at vcp.monash.edu.au
Wed Jul 14 03:00:40 CEST 2004


>How do you derive the values for these topology files?
>(e.g. charges, dihedrals, bonds)  are there any source
>that provide (some of) this information.

Lots of ways, depending on what the molecule is, previous work done on it etc:

         1/ Find them published somewhere in the literature for that 
molecule and your forcefield
         2/ Derive them for your forcefield from the literature for that 
molecule for another forcefield
         2/ Derive them from similar published molecules in the literature
         3/ Derive them from similar molecules within the rtp file of the 
forcefield you are using
         4/ Develop them from scratch yourself.

(Note pdb3gmx can actually handle any molecule, on the provision that the 
molecule appears in the residue file, *.rtp)

Catch ya,

Dr. Dallas Warren
Research Fellow
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 9083
When the only tool you own is a hammer, every problem begins to resemble a nail.

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