[gmx-users] residue not found

[abhisek Mondal]

Hi,
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
GROMACS*
*website at http://www.gromacs.org/Documentation/Errors
<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*

*INDIA*