GROMACS version:
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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) 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