Cannot add non-natural residues in charmm36 forcefield

User discussions
1

GROMACS version: gmx, 2020.4-MODIFIED
GROMACS modification: Yes

I tried to add non-standard residues in gromacs. I updated residuetypes.dat, generated the topology file with the non-natural residue and the two adjacent residues as a whole, modified the rtp and hdb file for the new residue. I have successfully used this method to add unnatural amino acids in amber99 forcefield. But when I used the same method in charmm36 forcefield, it feedback a lot errors:
ERROR2 [file topol. top, line 12284]: No default Bond types;
ERROR3 [file topol. top, line 49986]: No default U-B types;
ERROR30 [file topol. top, line 69670]: No default proper Dih. types;
Fatal error: Unknown cmap torsion between atoms 1526 1528 1530

Are there any noteworthy differences in the way unnatural residues are handled in amber and charmm force fields?

1 Like
2

It appears you have bonds between atom types that are not yet in the force field, so you need to add suitable parameters in ffbonded.itp and/or cmap.itp for the topology to be generated.

3

How did you go about solving it? Will be helpful if you could share.

4

Hi
I generated the parameter file using Amber tools, added the parameters to ffbonded.itp and edited all the required files as suggested in following Gromacs tutorial:
https://manual.gromacs.org/documentation/current/how-to/topology.html