When I use old charmm36 force field

User discussions
1

Dear GMX users,

I would like to ask about CHARMM36 force fields in GROMACS. When I use the old version fo charmm36 (CHARMM36-mar2019.ff), do I need to specify “define = -DUSE_OLD_C36” in mdp file?
or just need to download CHARMM36-jul2017.ff version?

Thanks for any advice.

Best regards,

Mijiddorj

2

You’ll get equivalent results. I suggest the March 2019 distribution with define = -DUSE_OLD_C36 in the .mdp file.

3

Dear Justin,

Thank you very much. I am using CHARMM36m and CHARMM36 for a D amino acid-containing peptides. When I define old C36 FF in my mdp file, there is an error message as:

ERROR 1 [file topol.top, line 615]:
Unknown cmap torsion between atoms 21 23 25 41 43

that corresponds to
C NH1 CTD1 C NH1 atom types.

In detail:
21 (C of L-AA) 23 (N of D-AA) 25 (CA of D-AA) 41 (C of D-AA) 43 (N of next L-AA)

I checked the cmap.itp. However, It was already defined this cmap.

How can I solve this problem?

Best regards,

Mijiddorj

4

There are parameters for D-amino acids in the updated CMAP terms that were refined in C36m. There is no support for D-amino acids in the port for the old C36. You could add it yourself if you need to. I won’t be able to get to that any time soon.

5

Dear Justin,

Thank you very much for your advice.

Best regards,
Mijiddorj