[gmx-users] residue not found

[Soham Sarkar]

Put your residue name in the residuetypes.dat file and designate it as
nucleic acid. Keep the same file in your ff folder, which in turn should be
in the working directory.

On Wed, 8 Aug 2018, 6:54 pm abhisek Mondal, <abhisek.mndl at gmail.com> wrote:

> 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*
> --
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