# Molecule name different in charmm-gui generated files **URL:** \ **Category:** User discussions\ **Created:** [July 20, 2024, 4:16pm UTC](https://gromacs.bioexcel.eu/t/molecule-name-different-in-charmm-gui-generated-files/9696 "2024-07-20T16:16:38Z")\ **Posts on this page:** 1\ **Page:** 1
**Author:** ![SP06](https://avatars.discourse-cdn.com/v4/letter/s/ecb155/32.png) [@SP06](https://gromacs.bioexcel.eu/u/SP06)\ **Post date:** [July 20, 2024, 4:16pm UTC](https://gromacs.bioexcel.eu/t/molecule-name-different-in-charmm-gui-generated-files/9696/1 "2024-07-20T16:16:38Z")
GROMACS version: GROMACS modification: Yes/No Here post your question : I generated topology files for cyclohexane from CHARMM-GUI. In the PDB file, the name is CYH, but in ipt file and .top file the name is CYHE. I found that on changing name of molecule to CYHE in PDB, the vmd visualization structure changes. SO, should I change the names in the .itp and .top file? I placed the itp file in the charmm36 forcefield folder in GROMACS. Does changing the name of molecule in .itp files affect subsequent steps in simulation? REMARK GENERATE LIGAND REMARK DATE: 7/20/24 5:46:24 CREATED BY USER: apache ATOM 1 C1 CYH C 1 -0.104 -0.151 0.004 1.00 0.00 CYHE ATOM 2 H11 CYH C 1 -0.360 -0.773 0.890 1.00 0.00 CYHE ATOM 3 H12 CYH C 1 -0.603 -0.610 -0.878 1.00 0.00 CYHE ATOM 4 C2 CYH C 1 1.425 -0.201 -0.181 1.00 0.00 CYHE ATOM 5 H21 CYH C 1 1.686 -1.075 -0.817 1.00 0.00 CYHE ATOM 6 H22 CYH C 1 1.899 -0.356 0.814 1.00 0.00 CYHE ATOM 7 C3 CYH C 1 2.013 1.077 -0.795 1.00 0.00 CYHE ATOM 8 H31 CYH C 1 1.628 1.168 -1.835 1.00 0.00 CYHE ATOM 9 H32 CYH C 1 3.120 0.989 -0.852 1.00 0.00 CYHE ATOM 10 C4 CYH C 1 1.649 2.358 -0.021 1.00 0.00 CYHE ATOM 11 H41 CYH C 1 1.585 3.192 -0.754 1.00 0.00 CYHE ATOM 12 H42 CYH C 1 2.463 2.608 0.695 1.00 0.00 CYHE ATOM 13 C5 CYH C 1 0.333 2.265 0.774 1.00 0.00 CYHE ATOM 14 H51 CYH C 1 -0.130 3.275 0.831 1.00 0.00 CYHE ATOM 15 H52 CYH C 1 0.567 1.944 1.814 1.00 0.00 CYHE ATOM 16 C6 CYH C 1 -0.674 1.269 0.184 1.00 0.00 CYHE ATOM 17 H61 CYH C 1 -1.575 1.219 0.834 1.00 0.00 CYHE ATOM 18 H62 CYH C 1 -0.996 1.652 -0.809 1.00 0.00 CYHE TER 19 CYHE 1 END ;; ;; Generated by CHARMM-GUI ([http://www.charmm-gui.org](http://www.charmm-gui.org)) v1.7 ;; ;; psf2itp\_mol.py ;; ;; Correspondance: ;; jul316@lehigh.edu or wonpil@lehigh.edu ;; ;; GROMACS topology file for CYHE ;; [moleculetype] ; name nrexcl CYHE 3 [atoms] ; nr type resnr residu atom cgnr charge mass ``` 1 CG321 1 CYHE C1 1 -0.180 12.0110 ; qtot -0.180 2 HGA2 1 CYHE H11 2 0.090 1.0080 ; qtot -0.090 3 HGA2 1 CYHE H12 3 0.090 1.0080 ; qtot 0.000 4 CG321 1 CYHE C2 4 -0.180 12.0110 ; qtot -0.180 5 HGA2 1 CYHE H21 5 0.090 1.0080 ; qtot -0.090 6 HGA2 1 CYHE H22 6 0.090 1.0080 ; qtot 0.000 7 CG321 1 CYHE C3 7 -0.180 12.0110 ; qtot -0.180 8 HGA2 1 CYHE H31 8 0.090 1.0080 ; qtot -0.090 9 HGA2 1 CYHE H32 9 0.090 1.0080 ; qtot 0.000 10 CG321 1 CYHE C4 10 -0.180 12.0110 ; qtot -0.180 11 HGA2 1 CYHE H41 11 0.090 1.0080 ; qtot -0.090 12 HGA2 1 CYHE H42 12 0.090 1.0080 ; qtot 0.000 13 CG321 1 CYHE C5 13 -0.180 12.0110 ; qtot -0.180 14 HGA2 1 CYHE H51 14 0.090 1.0080 ; qtot -0.090 15 HGA2 1 CYHE H52 15 0.090 1.0080 ; qtot 0.000 16 CG321 1 CYHE C6 16 -0.180 12.0110 ; qtot -0.180 17 HGA2 1 CYHE H61 17 0.090 1.0080 ; qtot -0.090 18 HGA2 1 CYHE H62 18 0.090 1.0080 ; qtot 0.000 ``` [bonds] ; ai aj funct b0 Kb ``` 1 2 1 1 3 1 1 4 1 1 16 1 4 5 1 4 6 1 4 7 1 7 8 1 7 9 1 7 10 1 ``` 10 11 1 10 12 1 10 13 1 13 14 1 13 15 1 13 16 1 16 17 1 16 18 1 [pairs] ; ai aj funct c6 c12 ``` 1 8 1 1 9 1 1 10 1 1 14 1 1 15 1 2 5 1 2 6 1 2 7 1 2 13 1 2 17 1 2 18 1 3 5 1 3 6 1 3 7 1 3 13 1 3 17 1 3 18 1 4 11 1 4 12 1 4 13 1 4 17 1 4 18 1 5 8 1 5 9 1 5 10 1 5 16 1 6 8 1 6 9 1 6 10 1 6 16 1 7 14 1 7 15 1 7 16 1 8 11 1 8 12 1 8 13 1 9 11 1 9 12 1 9 13 1 ``` 10 17 1 10 18 1 11 14 1 11 15 1 11 16 1 12 14 1 12 15 1 12 16 1 14 17 1 14 18 1 15 17 1 15 18 1 [angles] ; ai aj ak funct th0 cth S0 Kub ``` 2 1 3 5 2 1 4 5 2 1 16 5 3 1 4 5 3 1 16 5 4 1 16 5 1 4 5 5 1 4 6 5 1 4 7 5 5 4 6 5 5 4 7 5 6 4 7 5 4 7 8 5 4 7 9 5 4 7 10 5 8 7 9 5 8 7 10 5 9 7 10 5 7 10 11 5 7 10 12 5 7 10 13 5 ``` 11 10 12 5 11 10 13 5 12 10 13 5 10 13 14 5 10 13 15 5 10 13 16 5 14 13 15 5 14 13 16 5 15 13 16 5 ``` 1 16 13 5 1 16 17 5 1 16 18 5 ``` 13 16 17 5 13 16 18 5 17 16 18 5 [dihedrals] ; ai aj ak al funct phi0 cp mult ``` 2 1 4 5 9 2 1 4 6 9 2 1 4 7 9 3 1 4 5 9 3 1 4 6 9 3 1 4 7 9 2 1 16 13 9 2 1 16 17 9 2 1 16 18 9 3 1 16 13 9 3 1 16 17 9 3 1 16 18 9 4 1 16 13 9 4 1 16 17 9 4 1 16 18 9 5 4 1 16 9 6 4 1 16 9 7 4 1 16 9 1 4 7 8 9 1 4 7 9 9 1 4 7 10 9 5 4 7 8 9 5 4 7 9 9 5 4 7 10 9 6 4 7 8 9 6 4 7 9 9 6 4 7 10 9 4 7 10 11 9 4 7 10 12 9 4 7 10 13 9 8 7 10 11 9 8 7 10 12 9 8 7 10 13 9 9 7 10 11 9 9 7 10 12 9 9 7 10 13 9 7 10 13 14 9 7 10 13 15 9 7 10 13 16 9 ``` 11 10 13 14 9 11 10 13 15 9 11 10 13 16 9 12 10 13 14 9 12 10 13 15 9 12 10 13 16 9 10 13 16 17 9 10 13 16 18 9 14 13 16 17 9 14 13 16 18 9 15 13 16 17 9 15 13 16 18 9 ``` 1 16 13 10 9 1 16 13 14 9 1 16 13 15 9 ```