Error with "gmx grompp -f minim.mdp -c dmpc_npat.pdb -p topol_dmpc.top -o dmpc.tpr" command

lisadoesbiochemistry · April 20, 2023, 6:22pm

GROMACS version: gmx, version 2021.2
GROMACS modification: No

Hello fellow scientists,
I am having a problem running this command in GROMACS "“gmx grompp -f minim.mdp -c dmpc_npat.pdb -p topol_dmpc.top -o dmpc.tpr”

I am following this tutorial: KALP-15 in DPPC

I am trying to model a protein complex into dmpc lipid bilayers. I am not sure how to fix these errors. Whenever I try -maxwarn attachment to the end of command, it tells me “Error in user input:
Invalid command-line options In command-line option -maxwarn Too few (valid) values”

I also cannot perform “mdrun” command as it is not installed and I am not the admin. I will include my topol_dmpc.top and topol.top files at the end of the error message because they are the only ones I made modifications to. Please just use find to find the specific files. Thank you so much for your help! I am a newbie to this and all of this can be very confusing so I just want to let you know I truly appreciate your help.

This is my error message:
Command line:
gmx grompp -f minim.mdp -c dmpc_npat.pdb -p topol_dmpc.top -o dmpc.tpr

Ignoring obsolete mdp entry ‘ns_type’

NOTE 1 [file minim.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.

Setting the LD random seed to -318901771

WARNING 1 [file ffnonbonded.itp, line 1730]:
Bondtype LJ-14 was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.

old: 0.0003314 3.36e-07 0.0003314 3.36e-07
new: OW OW 1 0.0026173456 2.634129e-06

Generated 813 of the 2346 non-bonded parameter combinations

Excluding 3 bonded neighbours molecule type ‘DMPC’

Excluding 2 bonded neighbours molecule type ‘SOL’

WARNING 2 [file topol_dmpc.top, line 26]:
The GROMOS force fields have been parametrized with a physically
incorrect multiple-time-stepping scheme for a twin-range cut-off. When
used with a single-range cut-off (or a correct Trotter
multiple-time-stepping scheme), physical properties, such as the density,
might differ from the intended values. Since there are researchers
actively working on validating GROMOS with modern integrators we have not
yet removed the GROMOS force fields, but you should be aware of these
issues and check if molecules in your system are affected before
proceeding.

atom name 1 in topol_dmpc.top and dmpc_npat.pdb does not match (CN1 - CA)
atom name 1 in topol_dmpc.top and dmpc_npat.pdb does not match (CN1 - CA)

atom name 2 in topol_dmpc.top and dmpc_npat.pdb does not match (CN2 - CB)

atom name 3 in topol_dmpc.top and dmpc_npat.pdb does not match (CN3 - CC)

atom name 4 in topol_dmpc.top and dmpc_npat.pdb does not match (NTM - N)

atom name 5 in topol_dmpc.top and dmpc_npat.pdb does not match (CA - CD)

atom name 6 in topol_dmpc.top and dmpc_npat.pdb does not match (CB - CE)

atom name 12 in topol_dmpc.top and dmpc_npat.pdb does not match (CC - CF)

atom name 13 in topol_dmpc.top and dmpc_npat.pdb does not match (CD - CG)

atom name 30 in topol_dmpc.top and dmpc_npat.pdb does not match (CE - CH)

atom name 47 in topol_dmpc.top and dmpc_npat.pdb does not match (CN1 - CA)

atom name 48 in topol_dmpc.top and dmpc_npat.pdb does not match (CN2 - CB)

atom name 49 in topol_dmpc.top and dmpc_npat.pdb does not match (CN3 - CC)

atom name 50 in topol_dmpc.top and dmpc_npat.pdb does not match (NTM - N)

atom name 51 in topol_dmpc.top and dmpc_npat.pdb does not match (CA - CD)

atom name 52 in topol_dmpc.top and dmpc_npat.pdb does not match (CB - CE)

atom name 58 in topol_dmpc.top and dmpc_npat.pdb does not match (CC - CF)

atom name 59 in topol_dmpc.top and dmpc_npat.pdb does not match (CD - CG)

atom name 76 in topol_dmpc.top and dmpc_npat.pdb does not match (CE - CH)

atom name 93 in topol_dmpc.top and dmpc_npat.pdb does not match (CN1 - CA)

atom name 94 in topol_dmpc.top and dmpc_npat.pdb does not match (CN2 - CB)

(more than 20 non-matching atom names)

WARNING 3 [file topol_dmpc.top, line 26]:
1152 non-matching atom names
atom names from topol_dmpc.top will be used
atom names from dmpc_npat.pdb will be ignored

Analysing residue names:
There are: 128 Other residues
There are: 3655 Water residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups…
Number of degrees of freedom in T-Coupling group rest is 39591.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 52x52x56, spacing 0.119 0.119 0.119

Estimate for the relative computational load of the PME mesh part: 0.17

This run will generate roughly 1 Mb of data

There was 1 note

There were 3 warnings

topol_dmpc.top file:
;
; File ‘topol_dppc.top’ was generated
; By user: jalemkul (502)
; On host: bevany.biochem.vt.edu
; At date: Fri Oct 20 13:26:53 2006
;
; This is your topology file
;
; Include chain topologies
#include “/gpfs/home/lm18di/GROMACS/my_forcefield/gromos53a6_lipid.ff/forcefield.itp”
#include “dmpc.itp”

; Include water topology
#include “/gpfs/home/lm18di/GROMACS/my_forcefield/gromos53a6_lipid.ff/spc.itp”

; Include ion topologies
#include “/gpfs/home/lm18di/GROMACS/my_forcefield/gromos53a6_lipid.ff/ions.itp”

; System specifications
[ system ]
128-Lipid DPPC Bilayer

[ molecules ]
; molecule name nr.
DMPC 128
SOL 3655

topol.top file:
;
; File ‘topol.top’ was generated
; By user: lm18di (840232)
; On host: h22-login-25.rcc.fsu.edu
; At date: Thu Apr 20 13:10:57 2023
;
; This is a standalone topology file
;
; Created by:
; :-) GROMACS - gmx pdb2gmx, 2021.2 (-:
;
; Executable: /opt/rcc/gnu/bin/gmx
; Data prefix: /opt/rcc/gnu
; Working dir: /gpfs/home/lm18di/GROMACS/FtsQBL
; Command line:
; gmx pdb2gmx -f ranked_0_FtsQBL.pdb -o FtsQBL_processed.gro -ignh -ter -water spc
; Force field was read from the standard GROMACS share directory.
;

; Include forcefield parameters
#include “/gpfs/home/lm18di/GROMACS/my_forcefield/gromos53a6_lipid.ff/forcefield.itp”

; Include chain topologies
#include “topol_Protein_chain_A.itp”
#include “topol_Protein_chain_B.itp”
#include “topol_Protein_chain_C.itp”

; Include DMPC chain topology
#include “dmpc.itp”

; Include water topology
#include “/gpfs/home/lm18di/GROMACS/my_forcefield/gromos53a6_lipid.ff/spc.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 “/gpfs/home/lm18di/GROMACS/my_forcefield/gromos53a6.ff/ions.itp”

[ system ]
; Name
Protein

[ molecules ]
; Compound #mols
Protein_chain_A 1
Protein_chain_B 1
Protein_chain_C 1

lisadoesbiochemistry · April 20, 2023, 6:27pm

I already noticed one mistake under my topol_dmpc.top file unders [system], I changed DPPC to DMPC already. However, this is not resolving my problem. I know that pdb files will have different names for residues but I am not sure how to make the topol_dmpc.top file compatible with the dmpc_npat.pdb file. Also I am not sure if the first two errors are important or they can be ignored. Thanks again.

Karis · April 24, 2023, 5:10pm

This is purely from me trying the tutorial up to this step (so someone please correct me if I’m incorrect here), here’s what I found:

Regarding the differing names, it seems that the dmpc.itp file and the dmpc_npat.pdb file are giving different atom names. If you look in the first picture (or compare your files), you’ll notice that the column aname in dmpc.itp doesn’t match the names listed for atoms 1-46 (which describes 1 lipid in the bilayer) in the 3rd column of dmpc_npat.pdb.

Compare this to the atom names matching for dppc (in this case, atoms 1-50 describe 1 lipid in the bilayer)

As far as I can tell, this is just an issue with the naming convention, and it seems gromacs automatically chooses to stick with just one naming convention anyway (atom names from topol_dmpc.top will be used, atom names from dmpc_npat.pdb will be ignored), but if it turns out you need to use the names from the .pdb file instead of the ones in the .itp file, changing the names in the .itp file to match those in the .pdb file seems to make the error go away on my end.

Regarding the first warning, based on the description from the tutorial: “The so-called “Berger lipids” are somewhat of a hybrid between GROMOS atomtypes and OPLS partial charges. Since the long alkane chains are poorly represented by GROMOS bonded parameters, a Ryckaert-Bellemans dihedral potential is used, and a scaling factor of 0.125 is applied to Lennard-Jones 1-4 interactions.”, so if you’re following the tutorial, using the new parameters seems best. In the ffnonbonded.itp, you’ll find 2 lines describing the parameters for OW OW for whichever section line 1730 is under, one from the lipid parameters you copy-pasted in and one that was originally there. You can either use maxwarn to ignore as suggested by the error message, or just remove the line that was originally there, both just means you’re using the parameter you got from the lipid file.

For the second warning, that seems to be an issue with using GROMOS forcefields in general (From the error message I got: “Further information is available at GROMACS can not reproduce properties with the GROMOS force fields - Redmine #2884 (#2884) · Issues · GROMACS / GROMACS · GitLab, and a longer explanation of our decision to remove physically incorrect algorithms can be found at On The Importance of Accurate Algorithms for Reliable Molecular Dynamics Simulations | Theoretical and Computational Chemistry | ChemRxiv | Cambridge Open Engage .”) so someone else might need to help advise on whether this tutorial should still be followed as it is.

lisadoesbiochemistry · April 25, 2023, 6:07pm

Hello Karris,

How did you change the names in the .itp to match the ones in .pdb? Just copy and paste? I removed the OW OW line 1730, and then did -maxwarn 10, and then grompp worked.

Thank you so much! I was just wondering if by ignoring all warnings, that I wouldn’t run into further implications following the tutorial.

Karis · April 26, 2023, 4:50am

Yeah, just copy-pasted the names from the .pdb file to the .itp file so that the aname column in .itp matched the names of atoms 1-46 (representing 1 lipid) of the 3rd column in the .pdb file.

Regarding removing line 1730, did you check whether that was the line originally in the forcefield or the one that was added from the lipid parameters? To my understanding, it’s the one from the lipid parameters you want to keep.

Also regarding the issue with GROMOS forcefields, just keep in mind this could mean your simulation doesn’t result in realistic behavior

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Error with "gmx grompp -f minim.mdp -c dmpc_npat.pdb -p topol_dmpc.top -o dmpc.tpr" command

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