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: iitd...@gmail.com
Date: Thu, 11 Feb 2010 16:45:06 +0530
Subject: Re: [gmx-users] Software inconsistency error: Not enough water
To: gmx-users@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 <g...@hotmail.com
<mailto:g...@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: iitd...@gmail.com <mailto:iitd...@gmail.com>
Date: Thu, 11 Feb 2010 12:48:53 +0530
To: gmx-users@gromacs.org <mailto: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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