Hi:
I intended to find the rotation of one helix(more precisely, the
helical axis) in a protein MD trajectory. Here is the script I used in
ptraj module. But it seems that the rotation is much bigger than what I
see in VMD. What could be wrong?
trajin md_nvt3.crd.gz
center :173-316
image origin center
rms first out rms-avg-mon2 :173-316.CA
vector a1 :168-185.CA,C,O,N principal z out principal_a1
go
Thank you in advance!
Best,
Lishan
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Received on Wed Apr 12 2006 - 06:07:08 PDT
