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

[Chandan Choudhury]

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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