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

[Chandan Choudhury]

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> 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
> Date: Thu, 11 Feb 2010 12:48:53 +0530
> To: 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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