Dear All,
I want to calculate tilt angle of a peptide inserted
inside the lipid bilayer (i.e. angle between the
helical axis and bilayer normal). From previous posts
I got an idea that g_bundle wud solve my problem.
I am issuing the following on the command line:
g_bundle -f test.xtc -s test.tpr -na 2 -z -tu ps
This asks me to "Select a group of top and a group of
bottom atoms"
Group 0 ( System) has 12877 elements
Group 1 ( Protein) has 102 elements
Group 2 ( Protein-H) has 79 elements
Group 3 ( C-alpha) has 10 elements
Group 4 ( Backbone) has 31 elements
Group 5 ( MainChain) has 41 elements
Group 6 (MainChain+Cb) has 49 elements
Group 7 ( MainChain+H) has 54 elements
Group 8 ( SideChain) has 48 elements
Group 9 ( SideChain-H) has 38 elements
Group 10 ( Prot-Masses) has 102 elements
when I chose "1" and "1" it gives all angles as 90,
which is wrong and bun_tiltr is reported as "nan". The
manual says that "the program reads two index groups
and divides both of them in -na parts".
I am a lil confused! what should be my choice here?
regards,
Pri...
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