[gmx-users] fatal error [using pdb2gmx]

Dallas B. Warren Dallas.Warren at vcp.monash.edu.au
Wed Oct 26 02:10:27 CEST 2005

> I have a glyc.itp file for a single glycine molecule. It is 
> already included 
> in the glyc.top file for one glycine molecule. How can I use 
> these files to 
> get a topology file and a gromacs file (.top & .gro) for 200 
> molecules?? 
> does this mean that I don't need to use the 200glyc.pdb file for 200 
> molecules that I have?

If you have a topology file for a single glycine molecular then that is
all you need.  The same parameters etc are just duplicated for each
subsequent molecule in the large box.

For an example, just look how water is normally implimented.

Look in chapter 5 of the manual, that specifies what format to use in
the .itp file, then how to link that into the .top file.  Within the
.top file you simple include the .itp file for the single molecule, then
down the bottom specify how many of those molecule types are within the
simulation box.

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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