The solvent group SOL is not continuous

User discussions
1

GROMACS version: 2018.1
GROMACS modification: Yes/No

Hi, I would like to address a problem during a simulation of protein in ionic liquids. However, I have encountered an error where “The solvent group SOL is not continuous” during the gmx genion command.

In this simulation, I plan to retain the water crystals from the protein PDB file. May I know what should I do to solve this error?

The error is as below:

Group 5 ( MainChain) has 1269 elements
Group 6 ( MainChain+Cb) has 1560 elements
Group 7 ( MainChain+H) has 1558 elements
Group 8 ( SideChain) has 3066 elements
Group 9 ( SideChain-H) has 1055 elements
Group 10 ( Prot-Masses) has 4624 elements
Group 11 ( non-Protein) has 93066 elements
Group 12 ( Water) has 81966 elements
Group 13 ( SOL) has 81966 elements
Group 14 ( non-Water) has 15724 elements
Group 15 ( Other) has 11100 elements
Group 16 ( MOL) has 11100 elements
Select a group: 13
Selected 13: ‘SOL’

Program: gmx genion, version 2018.1
Source file: src/gromacs/gmxana/gmx_genion.cpp (line 486)

Fatal error:
The solvent group SOL is not continuous: index[858]=5482, index[859]=16583

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

The molecule section of topol.top is as below:

[ molecules ]
; Compound #mols
Protein_chain_A 1
SOL 286
cation 300
anion 300
SOL 27036

Thank you very much.

2

Hi,
gmx genion randomly replaces solvent molecules with monoatomic ions. The group of solvent molecules should be continuous and all molecules should have the same number of atoms.
In your case SOL(13) or Water(12) group is not continuous as you can see at the end of the topology file.
Depending on the difference between the first 286 water molecules and the others, an option is to define a new group in the index file having only the last 27036 water molecules (use gmx make_ndx to define a group in the index file) and then use such a group as input for gmx genion (that means that only water molecules of this group will be randomly replaced by ions)

Kind regards
Alessandra

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3

Dear Alessandra,

Alright, thank you very much for the suggestions. I will try on that to see if it works.

Sincerely,
Raymond

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