[gmx-users] residue not found

abhisek Mondal abhisek.mndl at gmail.com
Wed Aug 8 15:24:02 CEST 2018

I'm facing a very odd issue in gromacs. I'm trying to execute "pdb2gmx -f
dna1.pdb -o dna.gro" using AMBER/CHARMM forcefield, but getting the
following error:

*Program pdb2gmx, VERSION 4.6.2*
*Source code file: /home/user/gromacs-4.6.2/src/kernel/resall.c, line: 642*

*Fatal error:*
*Residue 'THY' not found in residue topology database*
*For more information and tips for troubleshooting, please check the
*website at http://www.gromacs.org/Documentation/Errors

I'm using DNA first time in gromacs.
What should be the residue name instead of the name of the bases I can't
understand. A little suggestion would be terrific here.

Thank you.

Abhisek Mondal

*Senior Research Fellow*
*Protein Crystallography Group*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*


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