Dear All,

I used SwissParm to generate CHARMM itp files for my ligand molecules. I used GROMACS for molecular dynamics simulations. After getting the itp file for the ligand, I used that file deleting [ atomtypes ] and [ pairtypes ].

Part of my itp file is as follows.

[ atoms ]

; nr type resnr resid atom cgnr charge mass

1 CB 1 LIG C 1 -0.1435 12.0110

2 CB 1 LIG C1 2 0.0825 12.0110

3 CB 1 LIG C2 3 0.0000 12.0110

4 CB 1 LIG C3 4 -0.1500 12.0110

5 CB 1 LIG C4 5 0.3100 12.0110

6 CB 1 LIG C5 6 -0.1500 12.0110

7 CB 1 LIG C7 7 -0.1500 12.0110

8 CB 1 LIG C8 8 -0.1435 12.0110

9 CB 1 LIG C9 9 0.3384 12.0110

10 NPYD 1 LIG N 10 -0.6200 14.0067

11 C=C 1 LIG C11 11 0.0806 12.0110

12 NC=O 1 LIG N1 12 -0.4691 14.0067

13 C=O 1 LIG C12 13 0.6156 12.0110

14 C=C 1 LIG C13 14 -0.1500 12.0110

15 C=C 1 LIG C14 15 -0.1238 12.0110

16 C=C 1 LIG C15 16 -0.1382 12.0110

My problem is CB, C=C like types are not in atomtypes.atp file. What is wrong with this file. Can anyone help me?

Thank you in advance.