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Hi,<br><br>genion in future Gromacs versions will only use the last SOL block<br>and give a proper error message when there is not enough water.<br><br>Berk<br><br><hr id="stopSpelling">From: iitdckc@gmail.com<br>Date: Thu, 11 Feb 2010 16:45:06 +0530<br>Subject: Re: [gmx-users] Software inconsistency error: Not enough water<br>To: gmx-users@gromacs.org<br><br><br clear="all">Thanks berk.<br>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.<br> [ molecules ]<br>; Compound #mols<br>
Protein_A 1<br>Protein_B 1<br>Protein_C 1<br>Protein_D 1<br>Protein_E 1<br>SOL 32<br>SOL 46<br>SOL 3<br>SOL 13<br>
SOL 19791<br>Na 48<br><br>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.<br><br>Chandan <br>
<br><br>--<br>Chandan kumar Choudhury<br>NCL, Pune<br>INDIA<br>
<br><br><div class="ecxgmail_quote">On Thu, Feb 11, 2010 at 3:38 PM, Berk Hess <span dir="ltr"><<a href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</a>></span> wrote:<br><blockquote class="ecxgmail_quote" style="padding-left: 1ex;">
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Hi,<br><br>This error message in incorrect, it is probably not a software inconsistency.<br>Looking at the code, it seems the problem is that the topology file<br>you provided does not have enough SOL molecules in the [molecules ] section.<br>
I'll fix this error message for the next release.<br><br>Berk<br><br><hr>From: <a href="mailto:iitdckc@gmail.com">iitdckc@gmail.com</a><br>Date: Thu, 11 Feb 2010 12:48:53 +0530<br>To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Subject: [gmx-users] Software inconsistency error: Not enough water<div><div></div><div class="h5"><br><br>Hello gmxusers !!<br>I am simulating a protein and it is bound to ATP.<br>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.<br>
Error:<br><br><br clear="all">$ genion -s em.tpr -o ion.pdb -p topol.top -np 48 <br>WARNING: turning of free energy, will use lambda=0 <br>Reading file em.tpr, VERSION 4.0.7 (single precision) <br>Using a coulomb cut-off of 0.9 nm <br>
Will try to add 48 Na ions and 0 Cl ions. <br>Select a continuous group of solvent molecules <br>Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat<br>Group 0 ( System) has 70056 elements <br>
Group 1 ( Protein) has 10214 elements <br>Group 2 ( Protein-H) has 5107 elements <br>Group 3 ( C-alpha) has 623 elements <br>
Group 4 ( Backbone) has 1869 elements <br>Group 5 ( MainChain) has 2488 elements <br>Group 6 (MainChain+Cb) has 3083 elements <br>
Group 7 ( MainChain+H) has 3099 elements <br>Group 8 ( SideChain) has 7115 elements <br>Group 9 ( SideChain-H) has 2619 elements<br>Group 10 ( Prot-Masses) has 10214 elements<br>
Group 11 ( Non-Protein) has 59842 elements<br>Group 12 ( ATP) has 43 elements<br>Group 13 ( SOL) has 59799 elements<br>Group 14 ( Other) has 59842 elements<br>Select a group: 13<br>Selected 13: 'SOL'<br>
Number of (3-atomic) solvent molecules: 19933<br><br>Processing topology<br><br>Back Off! I just backed up temp.top to ./#temp.top.1#<br><br>-------------------------------------------------------<br>Program genion, VERSION 4.0.7<br>
Source code file: gmx_genion.c, line: 269<br><br>Software inconsistency error:<br>Not enough water<br>-------------------------------------------------------<br><br>Though my system has sufficient amount of water (19933) molecules. Can not understand the error. Any information would be useful.<br>
<br><br>Chadan<br>--<br>Chandan kumar Choudhury<br>NCL, Pune<br>INDIA<br> <br></div></div><div class="ecxhm"><hr>Express yourself instantly with MSN Messenger! <a href="http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/">MSN Messenger</a></div>
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