GROMACS version:2023.3
GROMACS modification: No
hi i have multicopper oxidase protein with has C2O ligand (according to rcsb pdb its a ligand). So how can i add this in residuetypes.dat does it will accept LIG type and is there any other file file that i have to edit with this file
i have added C2O in residuetypes.dat as Lig now the error occurs and i am unable to find this residue topology database file
Writing topology
Back Off! I just backed up posre_Protein_chain_A.itp to ./#posre_Protein_chain_A.itp.3#
Processing chain 2 'B' (5 atoms, 3 residues)
Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully
-------------------------------------------------------
Program: gmx pdb2gmx, version 2021.4-Ubuntu-2021.4-2
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 597)
Fatal error:
Residue 'C2O' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
“Residue topology database” refers to .rtp files, you should follow the format specification to add your new residue there.
in which .rtp file i should add this new molecule there are so many .rtp files in gromacs with same name and few in charmm36 folder also
The one that belongs to the force field you’re using, it doesn’t really matter which if they’re divided into several independent files in the same directory, provided that you don’t need to add hydrogens or make a polymer.
hi i have added in cgenff.rtp file
[ C2O ]
;
[ atoms ]
CU1 CU 2.0000 1
CU2 CU 2.0000 2
O1 O -2.0000 3
[ bonds ]
CU1 O1
CU2 O1
[ angles ]
CU1 O1 CU2
and the gro file generated successfully but with i open gro file it shows this
It looks like a visualisation issue. .gro files do not contain any bond specification, so if the bond is longer than the visualisation program thinks is a normal bond length, the bonds will not show. I think you can probably change the bond distance. In VMD you definitely can, but that is pymol, right?
Are you sure you want your Cu2O with a +2 net charge?
Yeah, the charges could use some QM charge fitting with proper oxidation states, perhaps accounting for the immediate environment too.
In the .gro file, there will be no changes to the Cu2O moiety as you’re not adding any hydrogens. But make sure you treat the protonation on surrounding amino acids properly, whether they’re histidines or cysteines, and see whether you want them to be covalently or non-covalently bound.
