[gmx-users] Software inconsistency error: Not enough water

Berk Hess gmx3 at hotmail.com
Thu Feb 11 14:19:49 CET 2010 

Hi,

Yes, but genion is not smart enough (yet) to see the difference between crystal water and normal water.

Berk

> Date: Thu, 11 Feb 2010 13:07:41 +0000
> From: t.piggot at bristol.ac.uk
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Software inconsistency error: Not enough water
> 
> Plus I suppose that if you have kept the crystal waters you would not 
> want them to be replaced by genion.
> 
> Tom
> 
> Berk Hess wrote:
> > Hi,
> > 
> > We are getting to much detail now.
> > In principle yes, but since you get a clear error message now, I 
> > wouldn't worry about this.
> > The chance that the last water block is willingly smaller than the 
> > number of ions is about zero.
> > 
> > Berk
> > 
> >  > Date: Thu, 11 Feb 2010 13:34:59 +0100
> >  > From: erikm at xray.bmc.uu.se
> >  > To: gmx-users at gromacs.org
> >  > Subject: Re: [gmx-users] Software inconsistency error: Not enough water
> >  >
> >  > Hi,
> >  >
> >  > Is it desirable that genion only considers a single SOL block? Why not
> >  > use them all if there are many?
> >  >
> >  > Regards,
> >  >
> >  > Erik
> >  >
> >  > Berk Hess skrev:
> >  > > Hi,
> >  > >
> >  > > genion in future Gromacs versions will only use the last SOL block
> >  > > and give a proper error message when there is not enough water.
> >  > >
> >  > > Berk
> >  > >
> >  > > 
> > ------------------------------------------------------------------------
> >  > > From: iitdckc at gmail.com
> >  > > Date: Thu, 11 Feb 2010 16:45:06 +0530
> >  > > Subject: Re: [gmx-users] Software inconsistency error: Not enough water
> >  > > To: gmx-users at gromacs.org
> >  > >
> >  > >
> >  > > Thanks berk.
> >  > > By the way, if I dont give -p topol.top as input to genion, then
> >  > > genion executes. In this case, I manually edit the topology file and
> >  > > add the ion information.
> >  > > [ molecules ]
> >  > > ; Compound #mols
> >  > > Protein_A 1
> >  > > Protein_B 1
> >  > > Protein_C 1
> >  > > Protein_D 1
> >  > > Protein_E 1
> >  > > SOL 32
> >  > > SOL 46
> >  > > SOL 3
> >  > > SOL 13
> >  > > SOL 19791
> >  > > Na 48
> >  > >
> >  > > This is my part of topology after adding ions (Na). In the previous
> >  > > case of genion was only considering first SOL information, which has
> >  > > only 32 molecules.
> >  > >
> >  > > Chandan
> >  > >
> >  > >
> >  > > --
> >  > > Chandan kumar Choudhury
> >  > > NCL, Pune
> >  > > INDIA
> >  > >
> >  > >
> >  > > On Thu, Feb 11, 2010 at 3:38 PM, Berk Hess <gmx3 at hotmail.com
> >  > > <mailto:gmx3 at hotmail.com>> wrote:
> >  > >
> >  > > Hi,
> >  > >
> >  > > This error message in incorrect, it is probably not a software
> >  > > inconsistency.
> >  > > Looking at the code, it seems the problem is that the topology file
> >  > > you provided does not have enough SOL molecules in the [molecules
> >  > > ] section.
> >  > > I'll fix this error message for the next release.
> >  > >
> >  > > Berk
> >  > >
> >  > > 
> > ------------------------------------------------------------------------
> >  > > From: iitdckc at gmail.com <mailto:iitdckc at gmail.com>
> >  > > Date: Thu, 11 Feb 2010 12:48:53 +0530
> >  > > To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> >  > > Subject: [gmx-users] Software inconsistency error: Not enough water
> >  > >
> >  > >
> >  > > Hello gmxusers !!
> >  > > I am simulating a protein and it is bound to ATP.
> >  > > Simulation of protein alone (without) works fine. Solely ATP
> >  > > simulation too works. But the problem arises on adding ions to the
> >  > > protein + ATP (1QHH.pdb) file.
> >  > > Error:
> >  > >
> >  > >
> >  > > $ genion -s em.tpr -o ion.pdb -p topol.top -np 48
> >  > > WARNING: turning of free energy, will use lambda=0
> >  > > Reading file em.tpr, VERSION 4.0.7 (single precision)
> >  > > Using a coulomb cut-off of 0.9 nm
> >  > > Will try to add 48 Na ions and 0 Cl ions.
> >  > > Select a continuous group of solvent molecules
> >  > > Opening library file
> >  > > /usr/local/gromacs/share/gromacs/top/aminoacids.dat
> >  > > Group 0 ( System) has 70056
> >  > > elements
> >  > > Group 1 ( Protein) has 10214
> >  > > elements
> >  > > Group 2 ( Protein-H) has 5107
> >  > > elements
> >  > > Group 3 ( C-alpha) has 623
> >  > > elements
> >  > > Group 4 ( Backbone) has 1869
> >  > > elements
> >  > > Group 5 ( MainChain) has 2488
> >  > > elements
> >  > > Group 6 (MainChain+Cb) has 3083
> >  > > elements
> >  > > Group 7 ( MainChain+H) has 3099
> >  > > elements
> >  > > Group 8 ( SideChain) has 7115
> >  > > elements
> >  > > Group 9 ( SideChain-H) has 2619 elements
> >  > > Group 10 ( Prot-Masses) has 10214 elements
> >  > > Group 11 ( Non-Protein) has 59842 elements
> >  > > Group 12 ( ATP) has 43 elements
> >  > > Group 13 ( SOL) has 59799 elements
> >  > > Group 14 ( Other) has 59842 elements
> >  > > Select a group: 13
> >  > > Selected 13: 'SOL'
> >  > > Number of (3-atomic) solvent molecules: 19933
> >  > >
> >  > > Processing topology
> >  > >
> >  > > Back Off! I just backed up temp.top to ./#temp.top.1#
> >  > >
> >  > > -------------------------------------------------------
> >  > > Program genion, VERSION 4.0.7
> >  > > Source code file: gmx_genion.c, line: 269
> >  > >
> >  > > Software inconsistency error:
> >  > > Not enough water
> >  > > -------------------------------------------------------
> >  > >
> >  > > Though my system has sufficient amount of water (19933) molecules.
> >  > > Can not understand the error. Any information would be useful.
> >  > >
> >  > >
> >  > > Chadan
> >  > > --
> >  > > Chandan kumar Choudhury
> >  > > NCL, Pune
> >  > > INDIA
> >  > >
> >  > > 
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> >  >
> >  > --
> >  > -----------------------------------------------
> >  > Erik Marklund, PhD student
> >  > Laboratory of Molecular Biophysics,
> >  > Dept. of Cell and Molecular Biology, Uppsala University.
> >  > Husargatan 3, Box 596, 75124 Uppsala, Sweden
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> 
> -- 
> Thomas Piggot
> University of Bristol, UK.
> -- 
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