Where are restraints defined

User discussions
1

GROMACS version:2020.1 (Any)
GROMACS modification: No

I got the following error message:
.> ERROR 1 [file posre.itp, line 2]:
.> Incorrect number of parameters - found 5, expected 3 or 6 for Dih. Rest.
.> (after the function type).

As far as I know I have not set any dihedral restraints at all and I even tried adding a dihedral restraints section to my posre.itp file to no avail. So from which file could grompp get the idea that there are supposed to be dihedral restraints in my posre.itp file?

Commandline instruction:
gmx grompp -f nvt.mdp -c confout.gro -p topol.top -o nvt.tpr

posre.itp file contents:
; In this topology include file, you will find position restraint
; entries for all the heavy atoms in your original pdb file.
; This means that all the protons which were added by pdb2gmx are
; not restrained.

[ position_restraints ]
; atom type fx fy fz
2 1 1000 1000 1000
5 1 1000 1000 1000
6 1 1000 1000 1000
7 1 1000 1000 1000
9 1 1000 1000 1000
11 1 1000 1000 1000
15 1 1000 1000 1000
16 1 1000 1000 1000
17 1 1000 1000 1000
19 1 1000 1000 1000

[ dihedral_restraints ]

2

Adding [dihedral_restraints] when grompp is already complaining is not a viable solution. I see no way that grompp can misinterpret position restraints for dihedral restraints, because they are literally triggered by text saying [dihedral_restraints]. Please provide all input files (full .top and all #included .itp files) - there is something more complicated going on that can’t be determined by the snippet you’ve provided.

3

The other .itp files are part of charmm27 and I can try to locate them if necessary

4

I will need at least the posre.itp file, and ideally, your coordinates. I don’t need the charmm27.ff files as those are standard in the GROMACS distribution.

5

Oh, it’s full contents were pasted in the original post. The dihedral definition on the last line was the only thing added

6

As I am not near my computer, I cannot upload it at the moment.

7

The .gro file was of an Alanine dipeptide solvated system.

8

I understand that, but to diagnose the issue I need to run the command myself, which requires all the input files. There’s nothing in the topology that should trigger dihedral restraints so I do not understand where this error could be coming from. That’s why I’m asking for the inputs. Upload them whenever you can and I will look into it.

9

I’m sorry for taking so long. The Dropbox folder now contains the .gro file. I also included the .mdp file just in case I caused the error in that somehow.

10

Don’t bother searching, I don’t know what I originally did to foul things up, but it’s not in those files. I think I messed one of the files up previously and in bugsearching I must have removed the inclusion of the restriction file in the commandline, unknowingly unbroken the file original file and missed re-including the restriction file in the command line argument or something like that.