[gmx-users] How I can create a gromacs input file from a gamess output

Dallas Warren dallas.warren at vcp.monash.edu.au
Tue Jul 13 01:55:13 CEST 2004

>I 'd like your help to create a input file (.pdb, .gro,etc..) from a 
>gamess calculation result.
>I converted a xyz file from the z-matrix in gamess output to pdb with 
>but when I run pdb2gmx, the result is:
>"Fatal error: Residue 'UNK' not found in residue topology database"

You are getting that error because the molecule name within the pdb file is 
"UNK", and that is not a residue present within the force field that you 
are trying to generate the topology for.  If the molecule happens to be a 
residue in the force field you want to use, then simply change the "UNK" to 
the correct residue name.  However, more than likely the molecule isn't one 
in the list of residues available, therefore you will have to generate it 
all yourself (covered in the manual) and/or using the PRODRG server to 
generate one for you.

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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