Error during the inclusion of ions

User discussions
1

GROMACS version: 2018.1
GROMACS modification: Yes
Here post your question

Dear Gromacs users,

I converted both topology and structure files of my system from the Amber package to the Gromacs one. Therefore, I have the com.gro and com.top files. The next step was the inclusion of solvent molecules using the following command line:

gmx solvate -cp newbox.gro -cs spc216.gro -o com_solv.gro -p topol.top

The solvated structure and topology were successfully generated. However, I got an error during the inclusion of ions by using the following command line:

gmx grompp -f ions.mdp -c com_solv.gro -p com_solv.top -o ions.tpr

The error message was:

GROMACS: gmx grompp, version 2018.1
Executable: /usr/bin/gmx
Data prefix: /usr
Working dir: /home/eduardo/Documents/Projeto_Doutorado/Gromacs/Gromacs-cddp_CNH/AlignZ
Command line:
gmx grompp -f ions.mdp -c com_solv.gro -p com_solv.top -o ions.tpr

Setting the LD random seed to 797119382
Generated 171 of the 171 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 171 of the 171 1-4 parameter combinations

ERROR 1 [file com_solv.top, line 5337]:
Atomtype OW not found

Program: gmx grompp, version 2018.1
Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1390)

Fatal error:
There was 1 error in input file(s)

For more information and tips for troubleshooting, please check the GROMACS

The ions.mdp file was:

=============================================================
; ions.mdp - used as input into grompp to generate ions.tpr
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep = 0.01 ; Minimization step size
nsteps = 50000 ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist = 10 ; Frequency to update the neighbor list and long range forces
cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; Method to determine neighbor list (simple, grid)
coulombtype = cutoff ; Treatment of long range electrostatic interactions
rcoulomb = 1.0 ; Short-range electrostatic cut-off
rvdw = 1.0 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions

I verified that the OW type (oxygen atom of a SPC water molecule) was presented in both com_solv.gro and com_solv.top files.

I would like to know if anyone could help me with this error. If necessary, I can provide my input files (com_solv.gro and com_solv.top).

Sincerely,

Eduardo.

2

Hi,

I converted both topology and structure files of my system from the Amber package to the Gromacs one. Therefore, I have the com.gro and com.top files. The next step was the inclusion of solvent molecules using the following command line:

gmx solvate -cp newbox.gro -cs spc216.gro -o com_solv.gro -p topol.top

As input to gmx solvate you have to provide the molecule in a box and the topology (in your case -p com.top) if you want that the command add water molecules in the coordinate file and in the topology file.

My guess is that you got an error when running

gmx grompp -f ions.mdp -c com_solv.gro -p com_solv.top -o ions.tpr

since your topology does not contain water molecules. Note gmx solvate does not rename the *.top file, but just add a line in the given *.top

Best regards
Alessandra

1 Like
3

Dear Alessandra,

Thank you for your response. Actually, in order to include water molecules in the coordinate file (in a box) and in the topology file, I used:

gmx solvate -cp com_vac1.gro -cs spc216.gro -o com_solv.gro -p com_vac.top

As you mentioned, I renamed the topology file:

com_vac.top ---------> com_solv.top

After that, I tried to include ions:

gmx grompp -f ions.mdp -c com_solv.gro -p com_solv.top -o ions.tpr

Then, I got the error that I mentioned:

GROMACS: gmx grompp, version 2018.1
Executable: /usr/bin/gmx
Data prefix: /usr
Working dir: /home/eduardo/Documents/Projeto_Doutorado/Gromacs/Gromacs-cddp_CNH/AlignZ
Command line:
gmx grompp -f ions.mdp -c com_solv.gro -p com_solv.top -o ions.tpr

Setting the LD random seed to 1673495039
Generated 171 of the 171 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 171 of the 171 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type ‘CI1’
Excluding 3 bonded neighbours molecule type ‘CI2’
Excluding 3 bonded neighbours molecule type ‘CI3’
Excluding 3 bonded neighbours molecule type ‘CNH’

ERROR 1 [file com_solv.top, line 5337]:
No such moleculetype SOL

Program: gmx grompp, version 2018.1
Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 2439)

Fatal error:
There was 1 error in input file(s)

I verified the com_solv.top file and at the end of this file, I have:

[ system ]
; Name
Generic title in water

[ molecules ]
; Compound #mols
CI1 1
CI2 1
CI3 1
CNH 1
SOL 11105

Do you think I need to include a line in this file (com_solv.top) indicating the specific force field for these water molecules? I am asking this question, since the only mention of solvent molecules in this topology file is the “SOL” indicating the number of water molecules. The other parameters presented in this file refer to the solute.

Sincerely,

Eduardo.

4

A vacuum topology will not #include a water topology, so you cannot simply rename the file, you need to add a water model into it.

1 Like
5

Dear jalemkul,

I did not just rename the vaccum topology. Firstly, I had the topology (com_vac.top):

************************[ system ]
; Name
Generic title

[ molecules ]
; Compound #mols
CI1 1
CI2 1
CI3 1
CNH 1

After that, I solvated this system with the command:

gmx solvate -cp com_vac.gro -cs spc216.gro -o com_solv.gro -p com_vac.top

Now, this com_vac.top includes the water molecules:

[ system ]
; Name
Generic title in water

[ molecules ]
; Compound #mols
CI1 1
CI2 1
CI3 1
CNH 1
SOL 11105

The SOL refers to the 11105 water molecules that were included in my topology file. This way, I renamed this file only for indicating a new solvated topology: com_solv.top

Finally, I got an error during the inclusion of ions:

GROMACS: gmx grompp, version 2018.1
Executable: /usr/bin/gmx
Data prefix: /usr
Working dir: /home/eduardo/Documents/Projeto_Doutorado/Gromacs/Gromacs-cddp_CNH/AlignZ
Command line:
gmx grompp -f ions.mdp -c com_solv.gro -p com_solv.top -o ions.tpr

Setting the LD random seed to 1673495039
Generated 171 of the 171 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 171 of the 171 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type ‘CI1’
Excluding 3 bonded neighbours molecule type ‘CI2’
Excluding 3 bonded neighbours molecule type ‘CI3’
Excluding 3 bonded neighbours molecule type ‘CNH’

ERROR 1 [file com_solv.top, line 5337]:
No such moleculetype SOL

Program: gmx grompp, version 2018.1
Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 2439)

Fatal error:
There was 1 error in input file(s)

This new topology includes the water molecules, but it seems that the SOL (solvent) is not recognized as solvent molecules.

6

The new topology says that the associated coordinates now have water added, but it contains nothing to define the topology of those water molecules. That is your problem. Like I said, you need to manually #include a water topology into com_sol.top, you can’t just copy it from the vacuum topology and use it as input into gmx solvate.

1 Like
7

Dear jalemkul,

I will include a water topology into com_sol.top. Thank you for your help.

Sincerely,

Eduardo.

8

Dear jalemkul,

In order to define a water topology, I included the following line in com_solv.top:

; Include water topology
#include “oplsaa.ff/spc.itp”

[ system ]
; Name
Generic title in water

[ molecules ]
; Compound #mols
CI1 1
CI2 1
CI3 1
CNH 1
SOL 11105

Should I explicitly included the water topology in this file? For example, by adding the lines:

[ moleculetype ]
; molname nrexcl
SOL 2

[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 opls_116 1 SOL OW 1 -0.82
2 opls_117 1 SOL HW1 1 0.41
3 opls_117 1 SOL HW2 1 0.41

#ifndef FLEXIBLE
[ settles ]
; OW funct doh dhh
1 1 0.1 0.16330

[ exclusions ]
1 2 3
2 1 3
3 1 2
#else
[ bonds ]
; i j funct length force.c.
1 2 1 0.1 345000 0.1 345000
1 3 1 0.1 345000 0.1 345000

[ angles ]
; i j k funct angle force.c.
2 1 3 1 109.47 383 109.47 383
#endif

I am asking it, since I got an error when I used only the #include:

GROMACS: gmx grompp, version 2018.1
Executable: /usr/bin/gmx
Data prefix: /usr
Working dir: /home/eduardo/Documents/Projeto_Doutorado/Gromacs/Gromacs-cddp_CNH/AlignZ
Command line:
gmx grompp -f ions.mdp -c com_solv.gro -p com_solv.top -o ions.tpr

Setting the LD random seed to -407922730
Generated 171 of the 171 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 171 of the 171 1-4 parameter combinations

ERROR 1 [file spc.itp, line 7]:
Atomtype opls_116 not found
…

This opls_116 atomtype should be listed in the .gro file?

9

If you generated your original topology with AMBER, you can’t start mixing in OPLS-AA topologies with associated atom types. You should use an AMBER-compatible water topology.

10

Dear jalemkul,

I would like to thank you for your response. I’ll select an AMBER-compatible water topology.

Sincerely,

Eduardo.