GROMACS version: any
GROMACS modification: No
Dear all,
I encountered the following error using charmm36-jul2021.ff in gmx pdb2gmx with the protein from chain A from 4ake:
Residue 214 named GLY of a molecule in the input file was mapped
to an entry in the topology database, but the atom CB used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.
The problem is with the default (charged) C-terminus entry in aminoacids.c.tdb in both charmm36-jul2021.ff and charmm36_ljpme-jul2021.ff:
[ COO- ]
; standard C-terminus
[ replace ]
C C CC 12.011 0.34
O OT1 OC 15.9994 -0.67
OXT OT2 OC 15.9994 -0.67
[ add ]
2 8 OT C CA CB
OC 15.999400 -0.6700 -1
[ impropers ]
C CA OT2 OT1
In charmm36-feb2021.ff, the corresponding entry in merge.c.tdb has no such problem as there is N instead of CB:
; CHARMM CTER
[ COO- ]
[ replace ]
C C CC 12.011 0.34
O OT1 OC 15.9994 -0.67
OXT OT2 OC 15.9994 -0.67
[ add ]
2 8 OT C CA N
OC 15.9994 -0.67 -1
[ impropers ]
C CA OT2 OT1
It would be great if someone could replace this file on the Mackerell lab website. Alex Mackerell suggested Justin Lemkul may be able to help with this.
Many thanks
James