ERROR: Unknown left-hand XXXX in parameter file

User discussions
1

Hello I am completing Tutorial 1, Step Six: Equilibration and input:

gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr

and received the error:

WARNING 1 [file nvt.mdp, line 52]:
Unknown left-hand ‘\outl0\strokewidth0 \strokec2 title’ in parameter file

Prior to my input I created the .mdp textedit file below:

title = OPLS Lysozyme NVT equilibration
define = -DPOSRES ; position restrain the protein
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 50000 ; 2 * 50000 = 100 ps
dt = 0.002 ; 2 fs
; Output control
nstxout = 500 ; save coordinates every 1.0 ps
nstvout = 500 ; save velocities every 1.0 ps
nstenergy = 500 ; save energies every 1.0 ps
nstlog = 500 ; update log file every 1.0 ps
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; bonds involving H are constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Nonbonded settings
cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
DispCorr = EnerPres ; account for cut-off vdW scheme
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300 ; reference temperature, one for each group, in K
; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 300 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed

The GROMACS error website recommended:

Unknown left-hand XXXX in parameter file

[grompp] has found an unknown term in the .mdp file fed to it. You should check the spelling of XXXX and look for typographical errors. Be aware that quite a few run parameters changed between GROMACS 3.x and GROMACS 4.x and the output from grompp will sometimes offer helpful commentary about these situations.

Can somebody please assist me with what is wrong with my mdp file input into textedit?
I am using GROMACS: gmx grompp, version 2019.6

Thanks:)
Joel
mjsubach@ncsu.edu

2

The textedit program is a rich-text editor and will embed formatting characters into your files. Do not use word processing software or rich-text editors when dealing with plain-text simulation input/output files. You will break their format. Only use plain-text editors.

3

Hell jalemkul and thank you for your kind update and I used this same TextEdit (Version 1.12 (329)) for the same tutorial Step-4 Add Ions and did not have this problem, with you now knowing this would you still recommend a different TextEdit?

Kind Regards,
Joel

4

You shouldn’t have be using a text editor to make any changes to files. Maybe you saved before exiting when viewing one file but not another. But the advice remains - you cannot use a rich-text editor to manipulate any files that GROMACS reads. They will all break in the same way.

5

Hello and thanks a bunch for your kind update, its working now:)