[gmx-users] how to add c-terminal to the coarse-grained structure

[Rabeta Yeasmin]

Hi,

I am trying to convert all-atom system to coarse grained system using
martini. I am encountering a problem with the C terminal of the protein.


*Atom OT1 in residue LYS 45 was not found in rtp entry LYS with 22
atomswhile sorting atoms.*

This is because Lysine 45 is at the end of C-terminal and it has 23 atoms
due to -COOH, while in the rtp file of charmm36.ff, lysine has 22 atoms. I
am wondering how could I add n and c-terminal.

Thanks.

Rabeta Yeasmin