How to setup protein-ligand simulation using CHARMM-GUI for ligand preparation

Caterpillar
Thu, 02 Oct 2025 02:32:26 +0000
User discussions

GROMACS version: 2025.3
GROMACS modification: No

Goal:

I would like help getting the protein-ligand tutorial working with GROMACS 2025.3 and using CHARMM-GUI to produce the ligand parameters. I am stuck at the step of combining the ligand parameters with the protein setup.

What I’ve done so far:

Used the CHARMM-GUI Ligand Reader & Modeller to produce ligand parameters from a ligand .pdb file with hydrogens added. The output of that includes outputs gromacs/topol.top, gromacs/LIG.itp, gromacs/charmm36.itp, and ligandrm.pdb (transcribed at bottom).

I can then use gmx editconf to produce a corresponding .gro file for the ligand.

Following the instructions in the tutorial, I have created a 3HTB_processed.gro file, along with corresponding posres.itp and topol.top files.

Where I have issues:

When I try to combine the output of CHARMM-GUI with the protein files, attempting the solvation fails during the first call to gmx editconf, with the message:

Fatal error:

Invalid line in system.gro for atom 2615

Query:

How should I combine the ligand parameters output by CHARMM-GUI with the protein parameters produced by GROMACS?

My thanks to everyone reading.

gromacs/topol.top

;;
;; Generated by CHARMM-GUI (url removed) v1.7
;;
;; psf2itp_mol.py
;;
;; Correspondance:
;; jul316@lehigh.edu or wonpil@lehigh.edu
;;
;; The main GROMACS topology file
;;

; Include forcefield parameters
#include “charmm36.itp”
#include “LIG.itp”

[ system ]
; Name
Title

[ molecules ]
; Compound #mols
LIG 1

gromacs/LIG.itp

;;
;; Generated by CHARMM-GUI (url removed) v1.7
;;
;; psf2itp_mol.py
;;
;; Correspondance:
;; jul316@lehigh.edu or wonpil@lehigh.edu
;;
;; GROMACS topology file for LIG
;;

[ moleculetype ]
; name nrexcl
LIG 3

[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 CG331 1 LIG C1 1 -0.275 12.0110 ; qtot -0.275
2 HGA3 1 LIG H1 2 0.090 1.0080 ; qtot -0.185
3 HGA3 1 LIG H2 3 0.090 1.0080 ; qtot -0.095
4 HGA3 1 LIG H3 4 0.090 1.0080 ; qtot -0.005
5 CG2R61 1 LIG C2 5 -0.107 12.0110 ; qtot -0.112
6 HGR61 1 LIG H4 6 0.115 1.0080 ; qtot 0.003
7 CG2R61 1 LIG C3 7 -0.114 12.0110 ; qtot -0.111
8 HGR61 1 LIG H5 8 0.115 1.0080 ; qtot 0.004
9 CG2R61 1 LIG C4 9 -0.105 12.0110 ; qtot -0.101
10 HGR61 1 LIG H6 10 0.115 1.0080 ; qtot 0.014
11 CG2R61 1 LIG C5 11 0.109 12.0110 ; qtot 0.123
12 CG2R61 1 LIG C6 12 -0.117 12.0110 ; qtot 0.006
13 HGR61 1 LIG H7 13 0.115 1.0080 ; qtot 0.121
14 CG2R61 1 LIG C7 14 0.001 12.0110 ; qtot 0.122
15 CG321 1 LIG C8 15 -0.195 12.0110 ; qtot -0.073
16 HGA2 1 LIG H8 16 0.090 1.0080 ; qtot 0.017
17 HGA2 1 LIG H9 17 0.090 1.0080 ; qtot 0.107
18 CG321 1 LIG C9 18 -0.176 12.0110 ; qtot -0.069
19 HGA2 1 LIG H10 19 0.090 1.0080 ; qtot 0.021
20 HGA2 1 LIG H11 20 0.090 1.0080 ; qtot 0.111
21 OG311 1 LIG O 21 -0.531 15.9994 ; qtot -0.420
22 HGP1 1 LIG H12 22 0.420 1.0080 ; qtot -0.000

[ bonds ]
; ai aj funct b0 Kb
1 2 1
1 3 1
1 4 1
1 18 1
5 6 1
5 7 1
5 12 1
7 8 1
7 9 1
9 10 1
9 11 1
11 14 1
11 21 1
12 13 1
12 14 1
14 15 1
15 16 1
15 17 1
15 18 1
18 19 1
18 20 1
21 22 1

[ pairs ]
; ai aj funct c6 c12
1 14 1
1 16 1
1 17 1
2 15 1
2 19 1
2 20 1
3 15 1
3 19 1
3 20 1
4 15 1
4 19 1
4 20 1
5 10 1
5 11 1
5 15 1
6 8 1
6 9 1
6 13 1
6 14 1
7 13 1
7 14 1
7 21 1
8 10 1
8 11 1
8 12 1
9 12 1
9 15 1
9 22 1
10 14 1
10 21 1
11 13 1
11 16 1
11 17 1
11 18 1
12 16 1
12 17 1
12 18 1
12 21 1
13 15 1
14 19 1
14 20 1
14 22 1
15 21 1
16 19 1
16 20 1
17 19 1
17 20 1

[ angles ]
; ai aj ak funct th0 cth S0 Kub
2 1 3 5
2 1 4 5
2 1 18 5
3 1 4 5
3 1 18 5
4 1 18 5
6 5 7 5
6 5 12 5
7 5 12 5
5 7 8 5
5 7 9 5
8 7 9 5
7 9 10 5
7 9 11 5
10 9 11 5
9 11 14 5
9 11 21 5
14 11 21 5
5 12 13 5
5 12 14 5
13 12 14 5
11 14 12 5
11 14 15 5
12 14 15 5
14 15 16 5
14 15 17 5
14 15 18 5
16 15 17 5
16 15 18 5
17 15 18 5
1 18 15 5
1 18 19 5
1 18 20 5
15 18 19 5
15 18 20 5
19 18 20 5
11 21 22 5

[ dihedrals ]
; ai aj ak al funct phi0 cp mult
2 1 18 15 9
2 1 18 19 9
2 1 18 20 9
3 1 18 15 9
3 1 18 19 9
3 1 18 20 9
4 1 18 15 9
4 1 18 19 9
4 1 18 20 9
6 5 7 8 9
6 5 7 9 9
6 5 12 13 9
6 5 12 14 9
7 5 12 13 9
7 5 12 14 9
8 7 5 12 9
9 7 5 12 9
5 7 9 10 9
5 7 9 11 9
8 7 9 10 9
8 7 9 11 9
7 9 11 14 9
7 9 11 21 9
10 9 11 14 9
10 9 11 21 9
9 11 14 12 9
9 11 14 15 9
9 11 21 22 9
14 11 21 22 9
5 12 14 11 9
5 12 14 15 9
13 12 14 15 9
12 14 11 21 9
15 14 11 21 9
11 14 12 13 9
11 14 15 16 9
11 14 15 17 9
11 14 15 18 9
12 14 15 16 9
12 14 15 17 9
12 14 15 18 9
14 15 18 19 9
14 15 18 20 9
16 15 18 19 9
16 15 18 20 9
17 15 18 19 9
17 15 18 20 9
1 18 15 14 9
1 18 15 16 9
1 18 15 17 9

gromacs/charmm36.itp

;;
;; Generated by CHARMM-GUI (url removed) v1.7
;;
;; psf2itp_mol.py
;;
;; Correspondance:
;; jul316@lehigh.edu or wonpil@lehigh.edu
;;
;; CHARMM36 FF in GROMACS format
;;

[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 1.0 1.0

[ atomtypes ]
; name at.num mass charge ptype sigma epsilon ; sigma_14 epsilon_14
CG2R61 6 12.0110 -0.107 A 3.55005321205e-01 2.928800e-01
CG321 6 12.0110 -0.195 A 3.58141284692e-01 2.343040e-01 ; 3.38541512893e-01 4.184000e-02
CG331 6 12.0110 -0.275 A 3.65268474438e-01 3.263520e-01 ; 3.38541512893e-01 4.184000e-02
HGA2 1 1.0080 0.090 A 2.38760856462e-01 1.464400e-01
HGA3 1 1.0080 0.090 A 2.38760856462e-01 1.004160e-01
HGP1 1 1.0080 0.420 A 4.00013524445e-02 1.924640e-01
HGR61 1 1.0080 0.115 A 2.42003727796e-01 1.255200e-01
OG311 8 15.9994 -0.531 A 3.14487247504e-01 8.037464e-01

[ bondtypes ]
; i j func b0 Kb
CG2R61 CG2R61 1 1.375000e-01 2.552240e+05
CG2R61 CG321 1 1.490000e-01 1.924640e+05
CG2R61 CG331 1 1.490000e-01 1.924640e+05
CG2R61 HGR61 1 1.080000e-01 2.845120e+05
CG2R61 OG311 1 1.411000e-01 2.797422e+05
CG321 CG321 1 1.530000e-01 1.861880e+05
CG321 CG331 1 1.528000e-01 1.861880e+05
CG321 HGA2 1 1.111000e-01 2.585712e+05
CG321 OG311 1 1.420000e-01 3.581504e+05
CG331 CG331 1 1.530000e-01 1.861880e+05
CG331 HGA3 1 1.111000e-01 2.694496e+05
CG331 OG311 1 1.420000e-01 3.581504e+05
OG311 HGP1 1 9.600000e-02 4.560560e+05

[ pairtypes ]
; i j func sigma1-4 epsilon1-4
CG2R61 CG321 1 3.46773417049e-01 1.10698234855e-01
CG2R61 CG331 1 3.46773417049e-01 1.10698234855e-01
CG321 CG321 1 3.38541512893e-01 4.18400000000e-02
CG321 CG331 1 3.38541512893e-01 4.18400000000e-02
CG321 HGA2 1 2.88651184677e-01 7.82754725313e-02
CG321 HGA3 1 2.88651184677e-01 6.48182492821e-02
CG321 HGP1 1 1.89271432669e-01 8.97368027066e-02
CG321 HGR61 1 2.90272620344e-01 7.24690057887e-02
CG321 OG311 1 3.26514380198e-01 1.83381431383e-01
CG331 CG331 1 3.38541512893e-01 4.18400000000e-02
CG331 HGA2 1 2.88651184677e-01 7.82754725313e-02
CG331 HGA3 1 2.88651184677e-01 6.48182492821e-02
CG331 HGP1 1 1.89271432669e-01 8.97368027066e-02
CG331 HGR61 1 2.90272620344e-01 7.24690057887e-02
CG331 OG311 1 3.26514380198e-01 1.83381431383e-01

[ angletypes ]
; i j k func th0 cth S0 Kub
CG2R61 CG2R61 CG2R61 5 1.2000000e+02 3.3472000e+02 2.4162000e-01 2.9288000e+04
CG2R61 CG2R61 CG321 5 1.2000000e+02 3.8325440e+02 0.0000000e+00 0.0000000e+00
CG2R61 CG2R61 CG331 5 1.2000000e+02 3.8325440e+02 0.0000000e+00 0.0000000e+00
CG2R61 CG2R61 HGR61 5 1.2000000e+02 2.5104000e+02 2.1525000e-01 1.8409600e+04
CG2R61 CG2R61 OG311 5 1.2000000e+02 3.7823360e+02 0.0000000e+00 0.0000000e+00
CG2R61 CG321 CG2R61 5 1.0750000e+02 4.3346240e+02 0.0000000e+00 0.0000000e+00
CG2R61 CG321 CG321 5 1.0750000e+02 4.3346240e+02 0.0000000e+00 0.0000000e+00
CG2R61 CG321 CG331 5 1.0750000e+02 4.3346240e+02 0.0000000e+00 0.0000000e+00
CG2R61 CG321 HGA2 5 1.0750000e+02 4.1254240e+02 0.0000000e+00 0.0000000e+00
CG2R61 CG321 OG311 5 1.1010000e+02 6.3345760e+02 0.0000000e+00 0.0000000e+00
CG2R61 CG331 HGA3 5 1.0750000e+02 4.1254240e+02 0.0000000e+00 0.0000000e+00
CG2R61 OG311 HGP1 5 1.0800000e+02 5.4392000e+02 0.0000000e+00 0.0000000e+00
CG321 CG321 CG321 5 1.1360000e+02 4.8827280e+02 2.5610000e-01 9.3386880e+03
CG321 CG321 CG331 5 1.1500000e+02 4.8534400e+02 2.5610000e-01 6.6944000e+03
CG321 CG321 HGA2 5 1.1010000e+02 2.2175200e+02 2.1790000e-01 1.8853104e+04
CG321 CG321 OG311 5 1.1010000e+02 6.3345760e+02 0.0000000e+00 0.0000000e+00
CG321 CG331 HGA3 5 1.1010000e+02 2.8953280e+02 2.1790000e-01 1.8853104e+04
CG321 OG311 HGP1 5 1.0600000e+02 4.1840000e+02 0.0000000e+00 0.0000000e+00
CG331 CG321 CG331 5 1.1400000e+02 4.4643280e+02 2.5610000e-01 6.6944000e+03
CG331 CG321 HGA2 5 1.1010000e+02 2.8953280e+02 2.1790000e-01 1.8853104e+04
CG331 CG321 OG311 5 1.1010000e+02 6.3345760e+02 0.0000000e+00 0.0000000e+00
CG331 CG331 HGA3 5 1.1010000e+02 3.1380000e+02 2.1790000e-01 1.8853104e+04
CG331 OG311 HGP1 5 1.0600000e+02 4.8116000e+02 0.0000000e+00 0.0000000e+00
HGA2 CG321 HGA2 5 1.0900000e+02 2.9706400e+02 1.8020000e-01 4.5187200e+03
HGA3 CG331 HGA3 5 1.0840000e+02 2.9706400e+02 1.8020000e-01 4.5187200e+03
OG311 CG321 HGA2 5 1.0889000e+02 3.8409120e+02 0.0000000e+00 0.0000000e+00
OG311 CG331 HGA3 5 1.0889000e+02 3.8409120e+02 0.0000000e+00 0.0000000e+00

[ dihedraltypes ]
; i j k l func phi0 cp mult
CG2R61 CG2R61 CG2R61 CG2R61 9 1.800000e+02 1.297040e+01 2
CG2R61 CG2R61 CG2R61 CG321 9 1.800000e+02 1.297040e+01 2
CG2R61 CG2R61 CG2R61 CG331 9 1.800000e+02 1.297040e+01 2
CG2R61 CG2R61 CG2R61 HGR61 9 1.800000e+02 1.757280e+01 2
CG2R61 CG2R61 CG2R61 OG311 9 1.800000e+02 1.297040e+01 2
CG2R61 CG2R61 CG321 CG2R61 9 1.800000e+02 9.623200e-01 2
CG2R61 CG2R61 CG321 CG321 9 1.800000e+02 9.623200e-01 2
CG2R61 CG2R61 CG321 CG331 9 1.800000e+02 9.623200e-01 2
CG2R61 CG2R61 CG321 HGA2 9 0.000000e+00 8.368000e-03 6
CG2R61 CG2R61 CG321 OG311 9 0.000000e+00 0.000000e+00 2
CG2R61 CG2R61 CG331 HGA3 9 0.000000e+00 8.368000e-03 6
CG2R61 CG2R61 OG311 HGP1 9 1.800000e+02 4.142160e+00 2
CG2R61 CG321 CG321 CG321 9 0.000000e+00 1.673600e-01 3
CG2R61 CG321 CG321 CG331 9 0.000000e+00 1.673600e-01 3
CG2R61 CG321 CG321 CG331 9 0.000000e+00 1.673600e-01 3
CG2R61 CG321 CG321 HGA2 9 0.000000e+00 1.673600e-01 3
CG2R61 CG321 CG321 OG311 9 0.000000e+00 8.368000e-01 3
CG2R61 CG321 CG331 HGA3 9 0.000000e+00 1.673600e-01 3
CG2R61 CG321 OG311 HGP1 9 0.000000e+00 3.096160e+00 3
CG2R61 CG321 OG311 HGP1 9 0.000000e+00 5.857600e+00 2
CG2R61 CG321 OG311 HGP1 9 0.000000e+00 8.786400e+00 1
CG321 CG2R61 CG2R61 CG331 9 1.800000e+02 1.004160e+01 2
CG321 CG2R61 CG2R61 HGR61 9 1.800000e+02 1.004160e+01 2
CG321 CG2R61 CG2R61 OG311 9 1.800000e+02 1.004160e+01 2
CG321 CG321 CG321 CG321 9 0.000000e+00 2.698680e-01 2
CG321 CG321 CG321 CG321 9 0.000000e+00 3.957227e-01 4
CG321 CG321 CG321 CG321 9 0.000000e+00 4.707418e-01 5
CG321 CG321 CG321 CG321 9 1.800000e+02 6.265540e-01 3
CG321 CG321 CG321 CG331 9 0.000000e+00 4.528762e-01 4
CG321 CG321 CG321 CG331 9 0.000000e+00 6.297338e-01 2
CG321 CG321 CG321 CG331 9 0.000000e+00 8.531594e-01 5
CG321 CG321 CG321 CG331 9 1.800000e+02 3.402847e-01 3
CG321 CG321 CG321 HGA2 9 0.000000e+00 8.158800e-01 3
CG321 CG321 CG321 OG311 9 0.000000e+00 8.158800e-01 3
CG321 CG321 CG331 HGA3 9 0.000000e+00 6.694400e-01 3
CG321 CG321 OG311 HGP1 9 0.000000e+00 5.857600e-01 2
CG321 CG321 OG311 HGP1 9 0.000000e+00 1.004160e+00 3
CG321 CG321 OG311 HGP1 9 0.000000e+00 4.727920e+00 1
CG331 CG2R61 CG2R61 CG331 9 1.800000e+02 1.004160e+01 2
CG331 CG2R61 CG2R61 HGR61 9 1.800000e+02 1.004160e+01 2
CG331 CG2R61 CG2R61 OG311 9 1.800000e+02 1.004160e+01 2
CG331 CG321 CG321 CG331 9 0.000000e+00 1.597870e-01 2
CG331 CG321 CG321 CG331 9 1.800000e+02 1.329675e-01 6
CG331 CG321 CG321 HGA2 9 0.000000e+00 7.531200e-01 3
CG331 CG321 CG321 OG311 9 0.000000e+00 8.158800e-01 3
CG331 CG321 CG331 HGA3 9 0.000000e+00 6.694400e-01 3
CG331 CG321 OG311 HGP1 9 0.000000e+00 5.857600e-01 2
CG331 CG321 OG311 HGP1 9 0.000000e+00 1.004160e+00 3
CG331 CG321 OG311 HGP1 9 0.000000e+00 4.727920e+00 1
HGA2 CG321 CG321 HGA2 9 0.000000e+00 9.204800e-01 3
HGA2 CG321 CG331 HGA3 9 0.000000e+00 6.694400e-01 3
HGA2 CG321 OG311 HGP1 9 0.000000e+00 7.531200e-01 3
HGA3 CG331 CG331 HGA3 9 0.000000e+00 6.485200e-01 3
HGA3 CG331 OG311 HGP1 9 0.000000e+00 7.531200e-01 3
HGR61 CG2R61 CG2R61 HGR61 9 1.800000e+02 1.004160e+01 2
OG311 CG2R61 CG2R61 HGR61 9 1.800000e+02 1.004160e+01 2
OG311 CG2R61 CG2R61 OG311 9 1.800000e+02 1.414527e+01 2
OG311 CG321 CG321 HGA2 9 0.000000e+00 8.158800e-01 3
OG311 CG321 CG321 OG311 9 0.000000e+00 8.368000e-01 3
OG311 CG321 CG331 HGA3 9 0.000000e+00 6.694400e-01 3

[ dihedraltypes ]
; i j k l func q0 cq
CG2R61 CG2R61 CG2R61 OG311 2 0.000000e+00 1.255200e+02

ligandrm.pdb

REMARK GENERATE LIGAND
REMARK DATE: 10/ 1/25 16:55:28 CREATED BY USER: charmm-gui
ATOM 1 C1 LIG L 1 24.305 -24.087 -0.006 1.00 0.00 LIG
ATOM 2 H1 LIG L 1 23.647 -24.500 0.789 1.00 0.00 LIG
ATOM 3 H2 LIG L 1 24.180 -22.983 -0.031 1.00 0.00 LIG
ATOM 4 H3 LIG L 1 25.359 -24.317 0.255 1.00 0.00 LIG
ATOM 5 C2 LIG L 1 21.531 -27.253 -4.159 1.00 0.00 LIG
ATOM 6 H4 LIG L 1 21.072 -28.228 -4.096 1.00 0.00 LIG
ATOM 7 C3 LIG L 1 22.026 -26.786 -5.384 1.00 0.00 LIG
ATOM 8 H5 LIG L 1 21.948 -27.401 -6.268 1.00 0.00 LIG
ATOM 9 C4 LIG L 1 22.631 -25.524 -5.460 1.00 0.00 LIG
ATOM 10 H6 LIG L 1 23.026 -25.165 -6.400 1.00 0.00 LIG
ATOM 11 C5 LIG L 1 22.748 -24.730 -4.315 1.00 0.00 LIG
ATOM 12 C6 LIG L 1 21.652 -26.460 -3.009 1.00 0.00 LIG
ATOM 13 H7 LIG L 1 21.295 -26.833 -2.060 1.00 0.00 LIG
ATOM 14 C7 LIG L 1 22.258 -25.197 -3.078 1.00 0.00 LIG
ATOM 15 C8 LIG L 1 22.504 -24.431 -1.799 1.00 0.00 LIG
ATOM 16 H8 LIG L 1 21.791 -24.783 -1.020 1.00 0.00 LIG
ATOM 17 H9 LIG L 1 22.314 -23.350 -1.968 1.00 0.00 LIG
ATOM 18 C9 LIG L 1 23.950 -24.701 -1.360 1.00 0.00 LIG
ATOM 19 H10 LIG L 1 24.113 -25.804 -1.298 1.00 0.00 LIG
ATOM 20 H11 LIG L 1 24.660 -24.313 -2.128 1.00 0.00 LIG
ATOM 21 O LIG L 1 23.391 -23.478 -4.416 1.00 0.00 LIG
ATOM 22 H12 LIG L 1 23.432 -23.119 -3.524 1.00 0.00 LIG
TER 23 LIG 1
END

10 posts - 3 participants