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

[Berk Hess]

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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