@jalemkul We have a sort of niche application. I am trying to model a small acid-base system in water. I have previously run acetic acid and pyridine using the opslaa support. I am trying to adjust the relative strength of the acid and or base with similar molecules. In this step, I was trying to run a minimization on trifluoroacetic acid in order to generate an itp file for the molecule. I tried the same with 2-methylpyridine and I got the same error in reference to different lines.
I did generate a custom rtp file for the system I am working with following a tutorial for methane in water. The following shows the topology file generated using the pdb2gmx function.
;
; File ‘topol.top’ was generated
; By user: Ramson (1006)
; On host: mako
; At date: Fri Jul 2 19:29:47 2021
;
; This is a standalone topology file
;
; Created by:
; :-) GROMACS - gmx pdb2gmx, 2020.4 (-:
;
; Executable: /usr/local/gromacs/bin/gmx
; Data prefix: /usr/local/gromacs
; Working dir: /home/Ramson/2MP_Acetic_Water
; Command line:
; gmx pdb2gmx -f 2_Met_Pyr.pdb
; Force field was read from current directory or a relative path - path added.
;
; Include forcefield parameters
#include “./oplsaa_edit.ff/forcefield.itp”
[ moleculetype ]
; Name nrexcl
Other 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 2MP rtp 2MP q 0.0
1 opls_520 1 2MP N 1 -0.678 14.0067
2 opls_521 1 2MP C31 1 0.473 12.011
3 opls_521 1 2MP C32 1 0.473 12.011
4 opls_523 1 2MP C5 1 0.227 12.011
5 opls_522 1 2MP C41 1 -0.447 12.011
6 opls_522 1 2MP C42 1 -0.447 12.011
7 opls_525 1 2MP H61 1 0.155 1.008
8 opls_526 1 2MP H7 1 0.065 1.008
9 opls_525 1 2MP H62 1 0.155 1.008
10 opls_524 1 2MP H51 1 0.012 1.008
11 opls_670 1 2MP C6 1 -0.168 12.011
12 opls_140 1 2MP H8 1 0.06 1.008
13 opls_140 1 2MP H9 1 0.06 1.008
14 opls_140 1 2MP H10 1 0.06 1.008 ; qtot 0
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
1 3 1
2 5 1
2 10 1
3 6 1
3 11 1
4 5 1
4 6 1
4 8 1
5 7 1
6 9 1
11 12 1
11 13 1
11 14 1
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 4 1
1 7 1
1 9 1
1 12 1
1 13 1
1 14 1
2 6 1
2 8 1
2 11 1
3 5 1
3 8 1
3 10 1
4 10 1
4 11 1
5 9 1
6 7 1
6 12 1
6 13 1
6 14 1
7 8 1
7 10 1
8 9 1
9 11 1
[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 3 1
1 2 5 1
1 2 10 1
5 2 10 1
1 3 6 1
1 3 11 1
6 3 11 1
5 4 6 1
5 4 8 1
6 4 8 1
2 5 4 1
2 5 7 1
4 5 7 1
3 6 4 1
3 6 9 1
4 6 9 1
3 11 12 1
3 11 13 1
3 11 14 1
12 11 13 1
12 11 14 1
13 11 14 1
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
3 1 2 5 3
3 1 2 10 3
2 1 3 6 3
2 1 3 11 3
1 2 5 4 3
1 2 5 7 3
10 2 5 4 3
10 2 5 7 3
1 3 6 4 3
1 3 6 9 3
11 3 6 4 3
11 3 6 9 3
1 3 11 12 3
1 3 11 13 3
1 3 11 14 3
6 3 11 12 3
6 3 11 13 3
6 3 11 14 3
6 4 5 2 3
6 4 5 7 3
8 4 5 2 3
8 4 5 7 3
5 4 6 3 3
5 4 6 9 3
8 4 6 3 3
8 4 6 9 3
; Include Position restraint file
#ifdef POSRES
#include “posre.itp”
#endif
[ system ]
; Name
2-Methyl-Pyridine
[ molecules ]
; Compound #mols
Other 1
For reference, I am a beginner to gromacs. I am an undergraduate student working on this project as an independent study so my background knowledge on the subject is not immense. I would appreciate patience if I do not understand right away. Thank you!