[gmx-users] make a new bond in VERSION 4.5.4

Yulian Gavrilov zzeppelin87 at gmail.com
Tue Jul 5 17:41:10 CEST 2011

Thank you!

 I changed the residue names in the .pdb file to LYQ and GLQ

 LYQ NZ 1 GLQ C 1 0.13 LYQ GLQ

 pdb2gmx -f ubc7_94_t48_newgmx1.pdb -o processed.gro -water tip3p -chainsep
interactive -ignh -rtpres

Program pdb2gmx, VERSION 4.5.4

Source code file: resall.c, line: 581

 Fatal error:

Residue 'LYQ' not found in residue topology database

For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors


 I checked http://www.gromacs.org/Documentation/File_Formats/Topology_File

But as you see from the previous mail, I included LYQ and GLQ to the force
field. Maybe I missed something?



Yulian Gavrilov
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