Adding modified amino acids - pdb2gmx issue

User discussions
1

GROMACS version:2021.3
GROMACS modification: No
I have a (non-terminal) modified amino acid in my protein. I have already added the toplogy file in the aminoacids.rtp (attached) and put the protein label in residuetypes.dat. However, when I run pdb2gmx I get this error:
Fatal error:
Atom OXT in residue CRO 240 was not found in rtp entry CRO with 37 atoms
while sorting atoms.

I do not even have a OXT atom name in my CRO and its not a terminal residue, so not sure why its trying to find that perticular residue

CRO.rtp.dat (2.0 KB)

2

The atom O2 is being translated to OXT by xlateat.dat in $GMXLIB. Change its name to something else and it should work.

3

Thanks a lot, it works now.