Problem with repeating atom type in .itp file?

User discussions
1

GROMACS version: 2020.5
GROMACS modification: No
I am getting the following warning when I run a grompp for ion addition to my system.

  Atomtype OPLS_0 was defined previously (e.g. in the forcefield files),
  and has now been defined again. This could happen e.g. if you would use a
  self-contained molecule .itp file that duplicates or replaces the
  contents of the standard force-field files. You should check the contents
  of your files and remove such repetition. If you know you should override
  the previous definition, then you could choose to suppress this warning
  with -maxwarn.

The command I am executing is: gmx grompp -f ions.mdp -c nipaa-solv.gro -p topol.top -o ions.tpr -maxwarn 1 > ions.txt 2>&1

And this is my .itp file which is the source of the error:

[ atomtypes ]
; atm_kind symbol mass charge ptype sigma epsilon
TER H 1.0080 0.000 A 0.25000 0.12552
OPLS_0 C82 12.0110 0.000 A 0.35000 0.27614
OPLS_1 C81 12.0110 0.000 A 0.35000 0.27614
OPLS_2 H85 1.0080 0.000 A 0.25000 0.12552
OPLS_3 H85 1.0080 0.000 A 0.25000 0.12552
OPLS_4 H85 1.0080 0.000 A 0.25000 0.12552
OPLS_5 C17 12.0110 0.000 A 0.37500 0.43932
OPLS_6 O17 15.9990 0.000 A 0.29600 0.87864
OPLS_7 N18 14.0070 0.000 A 0.32500 0.71128
OPLS_8 H18 1.0080 0.000 A 0.00000 0.00000
OPLS_9 C17 12.0110 0.000 A 0.35000 0.27614
OPLS_10 H85 1.0080 0.000 A 0.25000 0.12552
OPLS_11 C80 12.0110 0.000 A 0.35000 0.27614
OPLS_12 H85 1.0080 0.000 A 0.25000 0.12552
OPLS_13 H85 1.0080 0.000 A 0.25000 0.12552
OPLS_14 H85 1.0080 0.000 A 0.25000 0.12552
OPLS_15 C80 12.0110 0.000 A 0.35000 0.27614
OPLS_16 H85 1.0080 0.000 A 0.25000 0.12552
OPLS_17 H85 1.0080 0.000 A 0.25000 0.12552
OPLS_18 H85 1.0080 0.000 A 0.25000 0.12552
OPLS_0 C82 12.0110 0.000 A 0.35000 0.27614
OPLS_1 C81 12.0110 0.000 A 0.35000 0.27614
OPLS_2 H85 1.0080 0.000 A 0.25000 0.12552
OPLS_3 H85 1.0080 0.000 A 0.25000 0.12552
OPLS_4 H85 1.0080 0.000 A 0.25000 0.12552
OPLS_5 C17 12.0110 0.000 A 0.37500 0.43932
OPLS_6 O17 15.9990 0.000 A 0.29600 0.87864
OPLS_7 N18 14.0070 0.000 A 0.32500 0.71128
OPLS_8 H18 1.0080 0.000 A 0.00000 0.00000
OPLS_9 C17 12.0110 0.000 A 0.35000 0.27614
OPLS_10 H85 1.0080 0.000 A 0.25000 0.12552
OPLS_11 C80 12.0110 0.000 A 0.35000 0.27614
OPLS_12 H85 1.0080 0.000 A 0.25000 0.12552
OPLS_13 H85 1.0080 0.000 A 0.25000 0.12552
OPLS_14 H85 1.0080 0.000 A 0.25000 0.12552
OPLS_15 C80 12.0110 0.000 A 0.35000 0.27614
OPLS_16 H85 1.0080 0.000 A 0.25000 0.12552
OPLS_17 H85 1.0080 0.000 A 0.25000 0.12552
OPLS_18 H85 1.0080 0.000 A 0.25000 0.12552
OPLS_0 C82 12.0110 0.000 A 0.35000 0.27614
OPLS_1 C81 12.0110 0.000 A 0.35000 0.27614
OPLS_2 H85 1.0080 0.000 A 0.25000 0.12552
OPLS_3 H85 1.0080 0.000 A 0.25000 0.12552
OPLS_4 H85 1.0080 0.000 A 0.25000 0.12552
OPLS_5 C17 12.0110 0.000 A 0.37500 0.43932
OPLS_6 O17 15.9990 0.000 A 0.29600 0.87864
OPLS_7 N18 14.0070 0.000 A 0.32500 0.71128
OPLS_8 H18 1.0080 0.000 A 0.00000 0.00000
OPLS_9 C17 12.0110 0.000 A 0.35000 0.27614
.
.
[ atoms ]
; srno atm_kind resnr res sym cgnr charge mass
1 TER 0 UNL H 1 0.060 1.0080
2 OPLS_0 1 UNL C82 1 -0.120 12.0110
3 OPLS_1 1 UNL C81 1 -0.120 12.0110
4 OPLS_2 1 UNL H85 1 0.060 1.0080
5 OPLS_3 1 UNL H85 1 0.060 1.0080
6 OPLS_4 1 UNL H85 1 0.060 1.0080
7 OPLS_5 1 UNL C17 1 0.500 12.0110
8 OPLS_6 1 UNL O17 1 -0.500 15.9990
9 OPLS_7 1 UNL N18 1 -0.500 14.0070
10 OPLS_8 1 UNL H18 1 0.300 1.0080
11 OPLS_9 1 UNL C17 1 0.140 12.0110
12 OPLS_10 1 UNL H85 1 0.060 1.0080
13 OPLS_11 1 UNL C80 1 -0.180 12.0110
14 OPLS_12 1 UNL H85 1 0.060 1.0080
15 OPLS_13 1 UNL H85 1 0.060 1.0080
16 OPLS_14 1 UNL H85 1 0.060 1.0080
17 OPLS_15 1 UNL C80 1 -0.180 12.0110
18 OPLS_16 1 UNL H85 1 0.060 1.0080
19 OPLS_17 1 UNL H85 1 0.060 1.0080
20 OPLS_18 1 UNL H85 1 0.060 1.0080
21 OPLS_0 2 UNL C82 1 -0.060 12.0110
22 OPLS_1 2 UNL C81 1 -0.120 12.0110
23 OPLS_2 2 UNL H85 1 0.060 1.0080
24 OPLS_3 2 UNL H85 1 0.060 1.0080
25 OPLS_4 2 UNL H85 1 0.060 1.0080
26 OPLS_5 2 UNL C17 1 0.500 12.0110
27 OPLS_6 2 UNL O17 1 -0.500 15.9990
28 OPLS_7 2 UNL N18 1 -0.500 14.0070
29 OPLS_8 2 UNL H18 1 0.300 1.0080
30 OPLS_9 2 UNL C17 1 0.140 12.0110
31 OPLS_10 2 UNL H85 1 0.060 1.0080
32 OPLS_11 2 UNL C80 1 -0.180 12.0110
33 OPLS_12 2 UNL H85 1 0.060 1.0080
.
.
.

It is essentially a monomer unit being repeated, and since the charges and everything is the same, I have given the units the same atm_type (OPLS_xx). What is the reason for this error? The error disappears when every atom in the polymer chain has a different number assigned to it ie OPLS_nnn where nnn is distinct for each atom.

2

Each atom type can only be defined once. You clearly have many redundancies in your [atomtypes] directive. Delete duplicate entries.