> > Stefan Hoorman wrote: > > > > Stefan Hoorman wrote: > > > I have tried using g_bundle in order to analyse helix axes in my > > > transmembran helices. I created two groups in my ndx file that > > included > > > the alpha carbons of the first half of my helix and a second > > group for > > > the alpha carbons for the second half. When I try using g_bundle > the > > > following error comes up: > > > "Fatal error: > > > The size of one of your index groups is not a multiple of n" > > > What am I doing wrong? > > > > Not a clue - What is your exact command line? How many atoms are in > > each index > > group? The value of n is the number of parts into which the axes > > are divided > > and there are several criteria in the code that must be met, else > > you get this > > error. So without this information, the best guess is: some > > criterion is not > > being met. > > > > -Justin > > > > > Thank you > > > > > > > -- > > > > g_bundle analyzes bundles of axes - and therefore number of atoms > > each group > > have to be divisible by number of axes (entered by -na). And I > > suppose, you > > are interested in analyzing only one axis, don't you? > > > > Milan > > > > > > Well, the exact command line was : g_bundle -f md.xtc -s md.tpr -z -n > > bundle.ndx > > As for analyzing one axis, yes, that is true, I am only interested in > > analysing my helix principal axis. > > 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. > > All analysis came up with the same error. > > > > You're not setting the -na flag, which by default is zero. In the code, if > the > value from -na (int n) is <= 0, you get the fatal error. Maybe the error > message should be made more specific, so that users actually know what n > is. > You need to explicitly set a value for -na >= 1. > > -Justin > > Right, thank you Justin, things worked out nicely now. I was able to calculatemy helix tilt with respect to the z axis. Would there be a way to calculate the tilt between two helix axes? I cannot simply calculate the tilt of each with respect to the z axis and subtract because the interhelical tilt does not depend only on the z axis. Can g_bundle give me that kind of information?
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