[gmx-users] Fatal Error: UNK

[Dallas B. Warren]

> I generated pdb file using Export to pdb function available 
> in Ghemical. When I ran pdb2gmx I get the following error,
> Fatal error: Residue 'UNK' not found in residue topology database
> Command line: pdb2gmx -f molecule.pdb -o molecule.gro -p molecule.top

If you open up the pdb file with a text editor you will see that the
residue/molecule you generated has the resname of UNK.  And since there
is no such residue in the forcefield database, it can't generate the
topology files.

Using pdb2gmx only works if the residue(s) are already in the forcefield
files.

Catch ya,

Dr. Dallas Warren
Lecturer
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
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