Error at grommp for ions.tpr

User discussions
1

GROMACS version: 2020.1
GROMACS modification: No
I was trying to prepare a system using dimethyl-sulfoxide as a solvent in oplsff after solvation step i am getting this error:-

Command line:
gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr -maxwarn 1

Ignoring obsolete mdp entry ‘title’
Ignoring obsolete mdp entry ‘ns_type’

NOTE 1 [file em.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 -717712930
Generated 330891 of the 330891 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 330891 of the 330891 1-4 parameter combinations

ERROR 1 [file dmso.itp, line 75]:
No default Ryckaert-Bell. types

ERROR 2 [file dmso.itp, line 76]:
No default Ryckaert-Bell. types

ERROR 3 [file dmso.itp, line 77]:
No default Ryckaert-Bell. types

ERROR 4 [file dmso.itp, line 78]:
No default Ryckaert-Bell. types

ERROR 5 [file dmso.itp, line 79]:
No default Ryckaert-Bell. types

ERROR 6 [file dmso.itp, line 80]:
No default Ryckaert-Bell. types

ERROR 7 [file dmso.itp, line 81]:
No default Ryckaert-Bell. types

ERROR 8 [file dmso.itp, line 82]:
No default Ryckaert-Bell. types

ERROR 9 [file dmso.itp, line 83]:
No default Ryckaert-Bell. types

ERROR 10 [file dmso.itp, line 84]:
No default Ryckaert-Bell. types

ERROR 11 [file dmso.itp, line 85]:
No default Ryckaert-Bell. types

ERROR 12 [file dmso.itp, line 86]:
No default Ryckaert-Bell. types

Excluding 3 bonded neighbours molecule type ‘Protein’
Excluding 3 bonded neighbours molecule type ‘LIG’

NOTE 2 [file topol.top, line 43922]:
System has non-zero total charge: -1.000000
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.

WARNING 1 [file topol.top, line 43922]:
You are using Ewald electrostatics in a system with net charge. This can
lead to severe artifacts, such as ions moving into regions with low
dielectric, due to the uniform background charge. We suggest to
neutralize your system with counter ions, possibly in combination with a
physiological salt concentration.

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof
Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net
Charge
J. Chem. Theory Comput. 10 (2014) pp. 381-393
-------- -------- — Thank You — -------- --------

There were 2 notes

There was 1 warning

Program: gmx grompp, version 2020.1
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1928)

Fatal error:
There were 12 errors in input file(s)

How can I fix this error?

2

Use coulombtype = cutoff for generating the input .tpr for genion. The warning message is actually irrelevant since you’re not actually doing dynamics with this topology. The more pressing issue is the missing dihedrals. You need to provide suitable parameters.

3

I use the OPLS 2015 version. I have the same problem of No default Ryckaert-Bell. types after running
gmx grompp -f ions.mdp -c Fab_solv.gro -p topol.top -o ions.tpr -maxwarn 1
using Justin’s ions.mdp file from his Lysosome tutorial.

Use coulombtype = cutoff in the ions.mdp file still has the same problem.

coulombtype = PME works fine for the OPLS 2001 version.

So is this an issue related to the OPLS 2015 version? How to resolve it?

4

@lanselibai what is in your system? What is(are) the missing dihedral(s)?

5

@jalemkul I have contacted Yale OPLS group. They said they are refining the OPLSAAM.

My system is a Fab protein (400 residues). I am not sure how to identify the missing dihedral.

Another thing I have found is,

  1. when “-inter” is used in the “gmx pdb2gmx”, the “No default Ryckaert-Bell. types” error still exists for “gmx grompp -f ions.mdp”.
  2. when “-inter” is not used in the “gmx pdb2gmx”, the “No default Ryckaert-Bell. types” error does not exist for “gmx grompp -f ions.mdp”.
6

Use of -inter doesn’t mean anything unless you made different selections when making the interactive selections. Maybe the difference is in a disulfide or something. But in any case, if a force field is missing dihedrals for common protein terms, it is not complete and therefore not ready for routine use.

7

Yes, I am not sure why -inter causes the differences. But anyway, I will wait for the refinement of OPLS/AAM

8

Use diff to compare the topologies and you’ll have your answer.

9

can you explain how to use diff for identifying missing dihedral s

10

@amoltagad115 in this instance, my advice is to simply generate two topologies and use diff to see which lines differ. This will indicate which lines call for interactions that are problematic.