Hi Justin,<br><br><br>Revisiting some of the calculations I had tried to do few days back.<br><br>Just as a recap I am trying to build a sphere around the protein.<br><br>As you had suggested in the last messgae of this thread to make a new directory. I did that.<br>
<br>I used the following commands:<br><br> editconf -f 1li.gro -c -box 15 15 15 -o onlyli.gro<br> genbox -cp onlyli.gro -cs mix.gro -shell 6 -o li_sol.gro<br> genbox -cp his1.gro -cs li_sol.gro <br><br><b><br>1li.gro is:</b><br>
1 Li ion<br> 1<br> 1LI+ LI 1 1.736 0.839 0.257<br> 1.86824 1.86824 1.86824<br><br><b>onlyli.gro is:</b><br>1 Li ion<br> 1<br> 1LI+ LI 1 7.500 7.500 7.500<br> 15.00000 15.00000 15.00000<br>
<br><b>mix.gro ( pre-made mix of 1:1 :: water: methanol)</b><br><br>li_sol.gro des look like a sphere after seeingin vmd.<br><br>his1.gro is:<br>UNNAMED<br> 14<br> 1HISH N 1 0.000 0.000 0.000<br> 1HISH H1 2 -0.033 0.000 -0.094<br>
1HISH H2 3 -0.033 -0.082 0.047<br> 1HISH CA 4 0.146 0.000 0.000<br> 1HISH CB 5 0.204 0.120 -0.077<br> 1HISH CG 6 0.291 0.076 -0.190<br> 1HISH ND1 7 0.240 0.009 -0.299<br>
1HISH HD1 8 0.145 -0.014 -0.315<br> 1HISH CD2 9 0.425 0.089 -0.215<br> 1HISH CE1 10 0.345 -0.019 -0.382<br> 1HISH NE2 11 0.458 0.027 -0.333<br> 1HISH HE2 12 0.549 0.020 -0.374<br>
1HISH C 13 0.195 0.000 0.146<br> 1HISH O 14 0.118 0.000 0.242<br> 2.50220 0.24060 2.47531<br><br><br><br>I get the following error yet again:<br><br>Fatal error:<br>One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off.<br>
<br><br>------------------------------------------------------<br><br>Thanks a lot in advance.<br><br>Sorry about reviving few days old thread.<br><br><br>Thanks,<br>SN<br><br><br><br><br><div class="gmail_quote">On Mon, May 9, 2011 at 6:21 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im"><br>
<br>
shivangi nangia wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi Justin,<br>
<br>
I used 15 nm cubic box and 6 nm shell.<br>
I again tried to insert only 1 histidine molecule in the sphere. I get the same error<br>
<br>
Fatal error:<br>
One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off.<br>
<br>
<br>
</blockquote>
<br></div>
Please provide the exact command that gives the error. I cannot reproduce this using a shell value less than half a box vector. You may also want to try starting from a clean directory - get rid of old files and intermediates so you're sure you're using the right files.<br>
<font color="#888888">
<br>
-Justin</font><div><div></div><div class="h5"><br>
<br>
-- <br>
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<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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