[gmx-users] the solvent group SOL is not continuous

Miguel Quiliano Meza rifaximina at gmail.com
Tue Jan 26 22:26:09 CET 2010

*Hi everyone.

I have a problem when I try to run GENION, GROMACS says:
WARNING: turning of free energy, will use lambda=0
Reading file 1x8a_solvatada.tpr, VERSION 3.3.3 (single precision)
Using a coulomb cut-off of 0.9 nm
Will try to add 0 Na ions and 15 NA+ ions.
Select a continuous group of solvent molecules
Opening library file /usr/share/gromacs/top/
Group     0 (      System) has 275439 elements
Group     1 (     Protein) has  1722 elements
Group     2 (   Protein-H) has  1371 elements
Group     3 (     C-alpha) has   185 elements
Group     4 (    Backbone) has   555 elements
Group     5 (   MainChain) has   741 elements
Group     6 (MainChain+Cb) has   909 elements
Group     7 ( MainChain+H) has   921 elements
Group     8 (   SideChain) has   801 elements
Group     9 ( SideChain-H) has   630 elements
Group    10 ( Prot-Masses) has  1722 elements
Group    11 ( Non-Protein) has 273717 elements
Group    12 (          ZN) has     1 elements
Group    13 (         SOL) has 273702 elements
Group    14 (         LIG) has    14 elements
Group    15 (       Other) has 273717 elements
Select a group: 13
Selected 13: 'SOL'

Program genion, VERSION 3.3.3
Source code file: ../../../../src/tools/gmx_genion.c, line: 429

Fatal error:
The solvent group SOL is not continuous: index[9]=1732, index[10]=1747

"Bad As This Shit Is, This Shit Ain't As Bad As You Think It Is." (Jackie

*I do not know the reason,the number of residues in top file and pdb file
are the same. The only warning that I saw was when I ran grompp:
WARNING 1 [file 1x8a.top, line unknown]:
  The largest charge group contains 11 atoms.
  Since atoms only see each other when the centers of geometry of the charge
  groups they belong to are within the cut-off distance, too large charge
  groups can lead to serious cut-off artifacts.
  For efficiency and accuracy, charge group should consist of a few atoms.
  For all-atom force fields use: CH3, CH2, CH, NH2 NH, OH, CO2, CO, etc.

*Coincidentally they are some of the atomos of my ligand*
I have been reading the web and no-one says nothing about it. I would be
very grateful if someone can help me or give me advices.

Best Regards
MIguel Quiliano*
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