[gmx-users] Residue not found in topology

[Bratin Kumar Das]

Hi
    In your tool.top file the particular lys molecule residue name you have
to modify. Then it will work..Actually grompp can't find the molecule in
the topology.

On Wed 22 Aug, 2018, 11:35 AM Amir Zeb, <zebamir85 at gmail.com> wrote:

> 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:
> /home/chip/Downloads/gromacs-5.1.4/src/gromacs/gmxpreprocess/resall.c,
> 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!
>
> Amir
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