Fatal Error: atom X in multiple T-coupling groups

User discussions
1

GROMACS version: 2020.6
GROMACS modification: Yes/No
I am getting this following error although I have added both the Protein/ Non protein groups
Fatal error:
Atom 4812 in multiple T-Coupling groups (1 and 2)
Kindly help me

2

What is atom 4812? What have you specified in your tc-grps setting? Somehow you have created two groups that overlap such that they both include this atom, which is not allowed.

3

I created an index file wherein I merged my protein and ligand molecules.
This is what I have specified in my tc groups

; Temperature coupling
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein_UNL non-Protein ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300 ; reference temperature, one for each group, in K

4

A ligand molecule falls within the default Non-Protein group. You need to create a different group that does not include the ligand if you are merging it with the Protein group.

5

Hi
I am also facing the same problem. I want to see the interaction between ligand and the specific residue of Protein. For that, I have created an additional group in index file named [R_001] which has the first 3563 atoms.

additional group in index.ndx

[R_001]
1 2 3 4 5 6 7 8 9 10 ....... 3563

in mdp file, I have defined two energy groups

in mdp file


tc-grps = Protein_LIG Water_and_ions
energygrps = LIG  R_001

I am facing the error “Atom 3453” in multiple Mon. groups (2 and 2).

I have checked both groups (LIG and R_001) thoroughly and found that 3453 is only in R_001. LIG doesn’t have Atom number 3453.

Why am I getting this error?

Thanks

6

A single protein residue should never span thousands of atoms. Your group is constructed incorrectly.

7

Hi @jalemkul
Thanks for your kind reply. However I fixed the problem.

I think there was some problem with the .ndx file writing system. When I deleted those atoms and re-write them manually it fixed the error.
(not sure though if it occurs again)

8

I faced similar problem I solved by making the index file again
gmx make_ndx -f em.gro -o index.ndx
then I select both protein and ligand 1|13
and created a new group
name 22 Protein_UNK
hit enter
reselect the newly created group i.e. 22
q
error was resolved