Addetive charmm36_2021 forcefield

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Hi, I am trying simulate a protein consist of cu+2 and NAG(a kind of sugar). I downloaded charmm36_2021 and modified it for cu+2 successfully, But For NAG. I renames BGLCNA in merg.rtp file and added hydrogens to .hdb file and NAG to resitype.dat as carb

When using pdb2gmx i counter this error:
Program: gmx pdb2gmx, version 2020
Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 902)

Fatal error:
The residues in the chain CU1500–NAG1512 do not have a consistent type. The
first residue has type ‘Ion’, while residue NAG1508 is of type ‘Carb’. Either
there is a mistake in your chain, or it includes nonstandard residue names
that have not yet been added to the residuetypes.dat file in the GROMACS
library directory. If there are other molecules such as ligands, they should
not have the same chain ID as the adjacent protein chain since it’s a separate
molecule.

How can resolve this issue?

Thanks.

2

Entities of different chain type need to be in different chains, e.g. separated by TER or by assigning different chain identifiers. If you need them to appear in the same [moleculetype], you can use the -merge feature of pdb2gmx.