GROMACS version: 2024.3-conda_forge
GROMACS modification: No
When I try to simulate a ligand with two proteins my system fails at the following stage, despite solvation and all prior steps reporting no issues whatsoever.
Command:
gmx grompp -f ions.mdp -c input_solv.pdb -p topol.top -o ions.tpr -maxwarn 1000
Error:
Command line:
gmx grompp -f ions.mdp -c input_solv.pdb -p topol.top -o ions.tpr -maxwarn 1000
NOTE 1 [file ions.mdp]:
For a correct single-point energy evaluation with nsteps = 0, use
continuation = yes to avoid constraining the input coordinates.
Setting the LD random seed to -1611696194
Generated 3081 of the 3081 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 3081 of the 3081 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
ERROR 1 [file topol.top, line 48]:
No such moleculetype M00
There was 1 NOTE
-------------------------------------------------------
Program: gmx grompp, version 2024.3-conda_forge
Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 2555)
Fatal error:
There was 1 error in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at https://manual.gromacs.org/current/user-guide/run-time-errors.html
-------------------------------------------------------
The most bizarre part about this issue is that when I simulate just the two proteins or a single protein with the ligand, I am able to get good results without any issues whatsoever. The issue only appears when all 3 molecules are present at once. It is also noteworthy to mention that ligand parameterization is done with acpype and the solvated complex does not contain any clashes or other irregularities.
topol.top
;
; File 'topol.top' was generated
; By user: unknown (0)
; On host: 5be101628e28
; At date: Wed Nov 27 05:11:33 2024
;
; This is a standalone topology file
;
; Created by:
; :-) GROMACS - gmx pdb2gmx, 2023.5 (-:
;
; Executable: /usr/local/gromacs/bin/gmx
; Data prefix: /usr/local/gromacs
; Working dir: /root/test
; Command line:
; gmx pdb2gmx -f input.pdb -o input_processed.pdb -water tip3p -ignh -missing
; Force field was read from the standard GROMACS share directory.
;
; Include forcefield parameters
#include "amber99sb-ildn.ff/forcefield.itp"
#include "clean_ligand_1.acpype/clean_ligand_1_GMX.itp"
; Include chain topologies
#include "topol_Protein_chain_A.itp"
#include "topol_Protein_chain_B.itp"
; Include water topology
#include "amber99sb-ildn.ff/tip3p.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include "amber99sb-ildn.ff/ions.itp"
[ system ]
; Name
Protein in water
[ molecules ]
; Compound #mols
Protein_chain_A 1
clean_ligand_1 1
Protein_chain_B 1
SOL 9078
clean_ligand_1.acpype/clean_ligand_1_GMX.itp
; clean_ligand_1_GMX.itp created by acpype (v: 2023.10.27) on Wed Nov 27 05:11:33 2024
[ atomtypes ]
;name bond_type mass charge ptype sigma epsilon Amb
nq nq 0.00000 0.00000 A 3.36510e-01 3.58987e-01 ; 1.89 0.0858
cy cy 0.00000 0.00000 A 3.39771e-01 4.51035e-01 ; 1.91 0.1078
c5 c5 0.00000 0.00000 A 3.39771e-01 4.51035e-01 ; 1.91 0.1078
ss ss 0.00000 0.00000 A 3.53241e-01 1.18156e+00 ; 1.98 0.2824
c3 c3 0.00000 0.00000 A 3.39771e-01 4.51035e-01 ; 1.91 0.1078
oh oh 0.00000 0.00000 A 3.24287e-01 3.89112e-01 ; 1.82 0.0930
n7 n7 0.00000 0.00000 A 3.50765e-01 2.18405e-01 ; 1.97 0.0522
c6 c6 0.00000 0.00000 A 3.39771e-01 4.51035e-01 ; 1.91 0.1078
h2 h2 0.00000 0.00000 A 2.24382e-01 8.70272e-02 ; 1.26 0.0208
h1 h1 0.00000 0.00000 A 2.42200e-01 8.70272e-02 ; 1.36 0.0208
ho ho 0.00000 0.00000 A 5.37925e-02 1.96648e-02 ; 0.30 0.0047
hn hn 0.00000 0.00000 A 1.10650e-01 4.18400e-02 ; 0.62 0.0100
hc hc 0.00000 0.00000 A 2.60018e-01 8.70272e-02 ; 1.46 0.0208
[ moleculetype ]
;name nrexcl
clean_ligand_1 3
[ atoms ]
; nr type resi res atom cgnr charge mass ; qtot bond_type
1 nq 1 M00 N1 1 -0.725600 14.01000 ; qtot -0.726
2 cy 1 M00 C1 2 0.228600 12.01000 ; qtot -0.497
3 c5 1 M00 C2 3 0.145500 12.01000 ; qtot -0.352
4 cy 1 M00 C3 4 0.311300 12.01000 ; qtot -0.040
5 cy 1 M00 C4 5 0.152500 12.01000 ; qtot 0.112
6 ss 1 M00 S1 6 -0.332200 32.06000 ; qtot -0.220
7 c5 1 M00 C5 7 0.056100 12.01000 ; qtot -0.164
8 c3 1 M00 C6 8 0.348900 12.01000 ; qtot 0.185
9 oh 1 M00 O1 9 -0.573800 16.00000 ; qtot -0.389
10 n7 1 M00 N2 10 -0.863202 14.01000 ; qtot -1.252
11 c3 1 M00 C7 11 -0.087600 12.01000 ; qtot -1.340
12 c3 1 M00 C8 12 -0.087600 12.01000 ; qtot -1.427
13 oh 1 M00 O2 13 -0.631300 16.00000 ; qtot -2.058
14 oh 1 M00 O3 14 -0.631300 16.00000 ; qtot -2.690
15 c3 1 M00 C9 15 0.387300 12.01000 ; qtot -2.302
16 c3 1 M00 C10 16 -0.103400 12.01000 ; qtot -2.406
17 oh 1 M00 O4 17 -0.601800 16.00000 ; qtot -3.008
18 c6 1 M00 C11 18 -0.058700 12.01000 ; qtot -3.066
19 c6 1 M00 C12 19 -0.073400 12.01000 ; qtot -3.140
20 c6 1 M00 C13 20 -0.073400 12.01000 ; qtot -3.213
21 c6 1 M00 C14 21 -0.076400 12.01000 ; qtot -3.290
22 c6 1 M00 C15 22 -0.076400 12.01000 ; qtot -3.366
23 c6 1 M00 C16 23 -0.076400 12.01000 ; qtot -3.442
24 h2 1 M00 H1 24 0.105700 1.00800 ; qtot -3.337
25 h1 1 M00 H2 25 0.067700 1.00800 ; qtot -3.269
26 h2 1 M00 H3 26 0.085700 1.00800 ; qtot -3.183
27 h1 1 M00 H4 27 0.095700 1.00800 ; qtot -3.088
28 h2 1 M00 H5 28 0.084700 1.00800 ; qtot -3.003
29 ho 1 M00 H6 29 0.421000 1.00800 ; qtot -2.582
30 hn 1 M00 H7 30 0.398800 1.00800 ; qtot -2.183
31 hc 1 M00 H8 31 0.051867 1.00800 ; qtot -2.131
32 hc 1 M00 H9 32 0.051867 1.00800 ; qtot -2.079
33 hc 1 M00 H10 33 0.051867 1.00800 ; qtot -2.027
34 hc 1 M00 H11 34 0.051867 1.00800 ; qtot -1.976
35 hc 1 M00 H12 35 0.051867 1.00800 ; qtot -1.924
36 hc 1 M00 H13 36 0.051867 1.00800 ; qtot -1.872
37 ho 1 M00 H14 37 0.420000 1.00800 ; qtot -1.452
38 ho 1 M00 H15 38 0.420000 1.00800 ; qtot -1.032
39 h2 1 M00 H16 39 0.050700 1.00800 ; qtot -0.981
40 hc 1 M00 H17 40 0.057700 1.00800 ; qtot -0.923
41 hc 1 M00 H18 41 0.057700 1.00800 ; qtot -0.866
42 ho 1 M00 H19 42 0.411000 1.00800 ; qtot -0.455
43 hc 1 M00 H20 43 0.065700 1.00800 ; qtot -0.389
44 hc 1 M00 H21 44 0.040450 1.00800 ; qtot -0.349
45 hc 1 M00 H22 45 0.040450 1.00800 ; qtot -0.308
46 hc 1 M00 H23 46 0.040450 1.00800 ; qtot -0.268
47 hc 1 M00 H24 47 0.040450 1.00800 ; qtot -0.227
48 hc 1 M00 H25 48 0.037450 1.00800 ; qtot -0.190
49 hc 1 M00 H26 49 0.037450 1.00800 ; qtot -0.152
50 hc 1 M00 H27 50 0.037450 1.00800 ; qtot -0.115
51 hc 1 M00 H28 51 0.037450 1.00800 ; qtot -0.077
52 hc 1 M00 H29 52 0.038700 1.00800 ; qtot -0.039
53 hc 1 M00 H30 53 0.038700 1.00800 ; qtot -0.000
...