Query regarding gmx error for sld.prm file while generating ions.tpr file

User discussions
1

GROMACS version:2020.3
GROMACS modification: Yes/No

when I am running the command:
$ gmx_mpi grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
I am getting error like:
ERROR 1 [file sld.prm, line 4]:
Unknown bond_atomtype CG2C1
How to sort out this

2

Where did this .prm file come from? Did you modify it in any way? CG2C1 is not a valid atom type in CGenFF.

3

.prm file will generate when we run the command ‘python cgenff_charmm2gmx.py JZ4 jz4_fix.mol2 jz4.str charmm36-mar2019.ff’. Can anyone please suggest to me, do we need to add hydrogens for docking complex separated protein-ligand files before starting MDS? Thanks in advance.

4

For CHARMM, which is an all-atom force field, yes.

5

Greetings!!!
Yes. I used CHARMM36 all-atom force field (July 2017)