Unknown cmap torsion

User discussions
,
1

GROMACS version: 2018
GROMACS modification: Yes/No

Dear all,
I’m simulating a large complex with several modified aminoacids, among these FME, a modified Met. I’m using charm36 ff, based on literature.
FME is the first residue of one of the chains.
From grompp I obtain the following error:
Unknown cmap torsion between atoms CG2O1 NH1 CT1 C N
(numbers are replaced with atomtypes)
I check the file cmap.itp, and the group “CG2O1 NH1 CT1 C NH1” is included, but not with N.

Where can I find the parameters for my group? Can these parameters be calculated?
For me it is the first time with charmm ff, so I have never worked with cmap parameters, but I cannot change the ff.
Suggestions?

Thank you
Federica

2

Combining CGenFF parameters with core protein force field parameters will often trigger these kinds of problems. CG2O1 is a carbonyl carbon type, so you can probably assume it can be copied from the standard CMAP parameters for C NH1 CT1 C NH1, but for modified residues, it’s worth checking. But doing that properly is very laborious.

3

Thanks for your reply.
I need to specify something, the modified residue is included in the native charmm36 ff, but lacks of this cmap parameters. Moreover, “the problematic atom” is N, not CG2O1, but the cmap.Itp file include a similar group: CG2O1 NH1 CT1 C NH1. I try to copy the parameters of this group, substituting NH1 with N, but this returns a long list of errors for other atoms.

Federica

4

No, CG2O1 is the problem. This is a CGenFF atom type and is not normally present in the backbone. It is a carbonyl carbon type, so it is supplanting the normal C in the C-NH1-CT1-C-N (I hadn’t noticed the last N type is for proline) CMAP parameter that is in cmap.itp. The solution I propose is to copy the entire contents of the C-NH1-CT1-C-N parameters and substitute in CG2O1 for the first C, so you have matching parameters.

5

Ok, many thanks for your reply!
Now the cmap error is solved, but a list of new errors has appeared.

6

Hey, how was the cmap error solved? I am getting a similar error.

7

Dear Shashank,
I solved the problem as indicated by Justin:
“The solution I propose is to copy the entire contents of the C-NH1-CT1-C-N parameters and substitute in CG2O1 for the first C, so you have matching parameters.”