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: er...@xray.bmc.uu.se
> To: gmx-users@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: iitd...@gmail.com
> > Date: Thu, 11 Feb 2010 16:45:06 +0530
> > Subject: Re: [gmx-users] Software inconsistency error: Not enough water
> > To: gmx-users@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 <g...@hotmail.com
> > <mailto:g...@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: iitd...@gmail.com <mailto:iitd...@gmail.com>
> > Date: Thu, 11 Feb 2010 12:48:53 +0530
> > To: gmx-users@gromacs.org <mailto:gmx-users@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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> > --
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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
> er...@xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys
>
> --
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