[gmx-users] Residue not found in topology

Amir Zeb zebamir85 at gmail.com
Wed Aug 22 08:04:49 CEST 2018

Hi gromacs users,

I want to simulate a protein where one of the lysine residues is modified
to acetylated lysine and has been denoted by KAC. I want to simulate it by
CharmM 36 ff, but it gave me this error.

Program gmx pdb2gmx, VERSION 5.1.4
Source code file:
line: 645

Fatal error:
Residue 'KAC' 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

Is CharmM 36 ff capable to simulate modified residue acetylated lysine?
If yes, what is the ff compatible notation for acetylated lysine?
If not, which ff can I use to simulate acetylated lysine?

Thanks in advance!


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