Error in adding ions using CHARMM36m

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Here post your question

Hi all,

I’m using gromcs with CHARMM36m ff. When I use an earlier CHARMM ff it works well.

When adding ions using
mpirun -np 1 gmx_mpi grompp -f ions.mdp -c pdb_solv.gro -p topol.top -o ions.tpr
it writes
ERROR 1 [file topol_Protein_chain_B.itp, line 1818]:
No default Proper Dih. types
This line is:
1 4 17 19 9
NH2-CT1-C-N

Might be related to terminal residue NH2.

Thank you for your time and consideration,
Best regards,
Asaf

2

Can you please specify which release you are using that has a problem, and which was correct? This parameter should have been added to the force field several years ago when users encountered the same problem.

3

Thanks a lot for your response. I really appreciate it.
Sure, I’m using gromacs/2020.2-cpu with charmm36-jul2021.
The previous one that works well with the same gromacs version is CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins).
This may be related to capping a terminal residue with NH2 in pdb2gmx etc.

Thank you for your time and consideration,
Best regards,
Asaf

4

I will look and see what is going on with CHARMM36; my statement before was that, to my knowledge, we had fixed this issue in the CHARMM36 port by introducing a parameter by analogy, which was included upstream in the parent CHARMM distribution. It therefore should have been included automatically in our latest port. I was hoping to track down where that might have been lost in the CHARMM36 lineage (which is distinct from the CHARMM27 files produced by the GROMACS team in 2010).

5

Great, thanks a lot. I really apprecaite it.
As a followup question there is the option to choose CT2 for the C terminal in gromacs -ter flag and we were wondering if:

  1. It means that it caps the residue to CT2?
  2. If so, is there an option to cap the N terminal with ACE?

Thank you again for your time and consideration,
Best regards,
Asaf

6

Yes.

Not via .tdb because there is limited ability to construct atoms. You need to have an actual ACE residue defined as the N-terminal species, and choose “None” as the terminus type when prompted.

7

Thanks a lot for your help.

Best regards,
Asaf