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

[Justin A. Lemkul]

Miguel Quiliano Meza wrote:
> *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/
> aminoacids.dat
> 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 Brown)
> 
> *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.
> 

Look at your coordinate file.  Do you have two separate blocks of solvent, like 
crystal waters and then solvent added by genbox (after your zinc and ligand, 
perhaps)?

-Justin

> Best Regards
> MIguel Quiliano*
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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