[gmx-users] Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus

[Atila Petrosian]

Dear David

Thanks for your quick reply

 This work includes 3 steps:

1) Making top file for protein WITHOUT ligand

2) Making top file for ligand

3) Merging 2 top file in a text editor (by including ligand.itp) and
obtaining a top file for complex.

My problem is about step (2): Ligand.itp should contain only GLN and not
NGLN-CGLN.

My question is that after removing extra atoms in ALA and renaming N
in ALA to O2, what remains is familiar for gromacs to build Ligand.itp
file?

Ligand in my system is a single GLN residue (which is both N- and C-
terminal residue) and not NGLN or GLN or CGLN residues.

NGLN or GLN or CGLN residues are default residues in rtp file and
there is not a single GLN residue (which is both N- and C- terminal
residue).



Best regards.