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

[Erik Marklund]

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
erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys