[gmx-users] pdb file format

Dallas Warren dallas.warren at vcp.monash.edu.au
Tue Feb 10 00:12:00 CET 2004


>Does someone can explaine to me how to set a pdf file?
>In fact I'm able to get it, but I don't what I should put for the 
>"resName" column. I'm studing an organic molecular crystal, I use babel to 
>convert a shelx file,  and it put "UNK" for the "resName" column. It seems 
>that pdb2gmx doesn't like that ...

You can only use pdb2gmx if the molecule, or components it is made up from, 
is known in the *.rtp file for the particular forcefield chosen.  The 
program has been set up to process and generate the topology file for 
proteins, so in it typically there are most of the residues.  If the 
residue name is one it doesn't know, then it will stop since it has no 
instructions on how to build the topology.  If a residue is missing, then 
you need to generate it yourself.  If you are dealing with another 
molecule, non-protein, then you need to generate the topology yourself or 
get it from someone else that has generated it.  As someone else mentioned, 
if you don't have the topology then you can use the PRODRG server to 
generate one for you and work from there.

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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