<b>Hi everyone.<br><br>I have a problem when I try to run GENION, GROMACS says:<br></b><br>WARNING: turning of free energy, will use lambda=0<br>Reading file 1x8a_solvatada.tpr, VERSION 3.3.3 (single precision)<br>Using a coulomb cut-off of 0.9 nm<br>
Will try to add 0 Na ions and 15 NA+ ions.<br>Select a continuous group of solvent molecules<br>Opening library file /usr/share/gromacs/top/<div id=":ue" class="ii gt">aminoacids.dat<br>Group 0 ( System) has 275439 elements<br>
Group 1 ( Protein) has 1722 elements<br>
Group 2 ( Protein-H) has 1371 elements<br>Group 3 ( C-alpha) has 185 elements<br>Group 4 ( Backbone) has 555 elements<br>Group 5 ( MainChain) has 741 elements<br>Group 6 (MainChain+Cb) has 909 elements<br>
Group 7 ( MainChain+H) has 921 elements<br>Group 8 ( SideChain) has 801 elements<br>Group 9 ( SideChain-H) has 630 elements<br>Group 10 ( Prot-Masses) has 1722 elements<br>Group 11 ( Non-Protein) has 273717 elements<br>
Group 12 ( ZN) has 1 elements<br>Group 13 ( SOL) has 273702 elements<br>Group 14 ( LIG) has 14 elements<br>Group 15 ( Other) has 273717 elements<br>Select a group: 13<br>
Selected 13: 'SOL'<br>
<br>-------------------------------------------------------<br>Program genion, VERSION 3.3.3<br>Source code file: ../../../../src/tools/gmx_genion.c, line: 429<br><br><span style="background-color: rgb(255, 255, 51);">Fatal error:</span><br style="background-color: rgb(255, 255, 51);">
<span style="background-color: rgb(255, 255, 51);">The solvent group SOL is not continuous: index[9]=1732, index[10]=1747</span><br>-------------------------------------------------------<br><br>"Bad As This Shit Is, This Shit Ain't As Bad As You Think It Is." (Jackie Brown)<br>
<br><b>I do not know the reason,the number of residues in top file and
pdb file are the same. The only warning that I saw was when I ran
grompp:<br></b><br>WARNING 1 [file 1x8a.top, line unknown]:<br> The largest charge group contains 11 atoms.<br>
Since atoms only see each other when the centers of geometry of the charge<br> groups they belong to are within the cut-off distance, too large charge<br> groups can lead to serious cut-off artifacts.<br> For efficiency and accuracy, charge group should consist of a few atoms.<br>
For all-atom force fields use: CH3, CH2, CH, NH2 NH, OH, CO2, CO, etc.<br><br><b>Coincidentally they are some of the atomos of my ligand</b><br><b><br>I
have been reading the web and no-one says nothing about it. I would be
very grateful if someone can help me or give me advices.<br>
<br>Best Regards<br>MIguel Quiliano</b><br>
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