<br><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Stefan Hoorman wrote:<br>
> I have tried using g_bundle in order to analyse helix axes in my<br>
> transmembran helices. I created two groups in my ndx file that included<br>
> the alpha carbons of the first half of my helix and a second group for<br>
> the alpha carbons for the second half. When I try using g_bundle the<br>
> following error comes up:<br>
> "Fatal error:<br>
> The size of one of your index groups is not a multiple of n"<br>
> What am I doing wrong?<br>
<br>
Not a clue - What is your exact command line? How many atoms are in each index<br>
group? The value of n is the number of parts into which the axes are divided<br>
and there are several criteria in the code that must be met, else you get this<br>
error. So without this information, the best guess is: some criterion is not<br>
being met.<br>
<br>
-Justin<br>
<br>
> Thank you<br>
><br>
<br>
--<br>
<br>
g_bundle analyzes bundles of axes - and therefore number of atoms each group<br>
have to be divisible by number of axes (entered by -na). And I suppose, you<br>
are interested in analyzing only one axis, don't you?<br>
<br>
Milan<br>
<br></blockquote><div><br>Well, the exact command line was : g_bundle -f md.xtc -s md.tpr -z -n bundle.ndx<br>As for analyzing one axis, yes, that is true, I am only interested in analysing my helix principal axis.<br>I have tried using different group sizes for the index group. I have tried using only carbon alpha for the first half and then for the second half (each had 15 alpha carbons), then I tried with all sorts of different groups, first five residues and last five residues, first fifteen residues and so on.<br>
All analysis came up with the same error.<br><br></div></div>