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

Berk Hess gmx3 at hotmail.com
Thu Feb 11 14:55:48 CET 2010 

Hi,

Yes, but there are (currently) two independent steps in genion.
First water is replaced using the index group that the users selected
and then the top file is edited. They two steps are independent.
There are no checks that the index group actually matches the topology
molecule sections (and strictly speaking they don't have to either).
But it would be better to link the two steps, although I don't think I want
to spend more time on this.

Berk

> Date: Thu, 11 Feb 2010 13:29:06 +0000
> From: t.piggot at bristol.ac.uk
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Software inconsistency error: Not enough water
> 
> Sure, that's why I think it is a good idea to do what you said and just 
> have genion use the final SOL block (normally added through genbox, so 
> not containing the crystal waters) rather than use all of the SOL blocks.
> 
> Tom
> 
> Berk Hess wrote:
> > 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
> >  > > > phone: +46 18 471 4537 fax: +46 18 511 755
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> >  > > >
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> >  >
> >  > --
> >  > Thomas Piggot
> >  > University of Bristol, UK.
> >  > --
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> -- 
> Thomas Piggot
> University of Bristol, UK.
> -- 
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