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