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

Berk Hess gmx3 at hotmail.com
Thu Feb 11 13:28:17 CET 2010


genion in future Gromacs versions will only use the last SOL block
and give a proper error message when there is not enough water.


From: iitdckc at gmail.com
Date: Thu, 11 Feb 2010 16:45:06 +0530
Subject: Re: [gmx-users] Software inconsistency error: Not enough water
To: gmx-users at 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 kumar Choudhury
NCL, Pune

On Thu, Feb 11, 2010 at 3:38 PM, Berk Hess <gmx3 at hotmail.com> wrote:


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.


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.


$ 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.

Chandan kumar Choudhury
NCL, Pune
Express yourself instantly with MSN Messenger! MSN Messenger


gmx-users mailing list    gmx-users at gromacs.org


Please search the archive at http://www.gromacs.org/search before posting!

Please don't post (un)subscribe requests to the list. Use the

www interface or send it to gmx-users-request at gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Express yourself instantly with MSN Messenger! Download today it's FREE!
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100211/e6069009/attachment.html>

More information about the gromacs.org_gmx-users mailing list