Hi,
Could it be that you have multiple SOL entries in the [ molecules ] section,
a first one for the crystal waters, with less than 48 molecules and then
one with the rest of the waters?
In that case genion should subtract the water molecules from the last SOL entry,
the current version takes the first SOL entry.
Berk
From: g...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] Software inconsistency error: Not enough water
Date: Thu, 11 Feb 2010 11:08:38 +0100
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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