[gmx-users] error

Dallas Warren dallas.warren at vcp.monash.edu.au
Tue Oct 14 04:23:00 CEST 2003


>"Fatal error: Residue '' not found in residue topology database."
>I kind of expected it, I imagine that these ff do not have defined at 
>least one
>atomtype that I need for my molecule.

It isn't the atomtype, more the fact that it doesn't know the residue.

>Where from to start fixing the problem?

You need to generate your own topology for the molecule.  So you need to 
define atom types, partial charges, bond length and constant, dihedrals 
etc.  The manual goes through the format needs for topologies and there are 
quite a few discussions here on the list.  First you need to settle on the 
forcefield to use, then use that to build the molecule.

The error you are encountering is using pdb2gmx, which when you build your 
own topologies you don't need to do.  That step is to build the topology of 
a protein that is built out of different residues quickly and easily.

>Does one really need the residue topology database?

No.  It is just a handy tool to use with long proteins that are made up of 
residues that fit together.  Helps to automate the generation of the topology.

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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