<div>you might have deleted just one atom of water molecule.</div>
<div>Ex: If you are using SPC water , you have to delete all 3 atoms in index file.</div>
<div> </div>
<div> </div>
<div>Best way is to make changes in .gro file..</div>
<div>Renumber the resulting .gro file using genconf, make a new index file and start running.<br><br> </div>
<div><span class="gmail_quote">On 10/10/06, <b class="gmail_sendername">Una Bjarnadottir</b> <<a href="mailto:una.bjarnadottir@ucd.ie">una.bjarnadottir@ucd.ie</a>> wrote:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Dear users,<br><br>In some of my simulations after neutralizing the systems with genion 2<br>of the ions were inside the active site cleft of the protein.
<br>In the discussion on the list it was commented to either delete the<br>solvent within the protein which I did I deleted the water molecule<br>(11798) and gave genion that index file as input but than this error came:<br>
<br>Fatal error: The solvent group is not continuous: index[8198]=11797,<br>index[8199]=11799<br><br>I don't want to use the -random command in genion if possible because in<br>none of the other simulations I have used it.
<br><br>Is there any other way to delete the solvent within the protein did I<br>misunderstand that so those water molecules will not be replaced?<br><br>Best regards, Una Bjarnadottir<br><br>_______________________________________________
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</a><br></blockquote></div><br><br clear="all"><br>-- <br>Viswanadham Sridhara,<br>Research Assistant,<br>Old Dominion University,<br>Norfolk, Va-23529.