<p>Hi Marc,</p>
<p>I think that -zeroq ignores the indexing. Using an index will extract a .tpr for the index group only, which is not what you want. There is no simple way to do what you want (using tpbconv). You'll have to modify the charge in the .top file and generate a new .tpr</p>
<p>Cheers,</p>
<p>Tsjerk</p>
<p><blockquote type="cite">On Sep 30, 2011 3:05 AM, "Marc Charendoff" <<a href="mailto:mcharend@sbcglobal.net">mcharend@sbcglobal.net</a>> wrote:<br><br><div><div style="font-family:arial, helvetica, sans-serif;font-size:10pt;color:#000000">
<div>Hello,</div><div><br></div><div> I'm trying to turn off a Na+ charge using tpbconv in 4.5.4. There is only one Na+ counterion in my simulation. I create an index file, run tpbconv, and my output file looks like the following:</div>
<div><br></div><div>[mcharend@xanadu C4_IS]$ tpbconv -s md.tpr -o mdn.tpr -n index.ndx -zeroq</div><div><br></div><div>.<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>.</div>
<div><br></div><div><div>Reading toplogy and stuff from md.tpr</div><div>Reading file md.tpr, VERSION 4.5.4 (single precision)</div><div>500000 steps (1000 ps) remaining from first run.</div><div>Group 0 (
System) has 3037 elements</div><div>Group 1 ( Other) has 15 elements</div><div>Group 2 ( DRG) has 15 elements</div><div>Group 3 ( NA+) has 1 elements</div><div>Group 4 ( Water) has 3021 elements</div>
<div>Group 5 ( SOL) has 3021 elements</div><div>Group 6 ( non-Water) has 16 elements</div><div>Group 7 ( Ion) has 1 elements</div><div>Group 8 ( DRG) has 15 elements</div>
<div>Group 9 ( NA+) has
1 elements</div><div>Group 10 ( Water_and_ions) has 3022 elements</div><div>Group 11 ( NA+) has 1 elements</div><div>Select a group: 9</div><div>Selected 9: 'NA+'</div><div>Segmentation fault</div>
<div>[mcharend@xanadu C4_IS]$ </div></div><div><br></div><div>The bottom of my index.ndx file looks like:</div><div><br></div><div>.<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span></div>
<div><br></div><div><div>[ NA+ ]</div><div>3037</div></div><div><br></div><div>Guidance appreciated. </div><div><br></div><div>Thanks , Marc</div><div></div>
</div></div><br>--<br>
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