AMBER Archive (2006)

Subject: AMBER: "vector" command in ptraj

From: Lishan Yao (yaolisha_at_msu.edu)
Date: Mon Apr 10 2006 - 13:20:56 CDT

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_at_CA
vector a1 :168-185_at_CA,C,O,N principal z out principal_a1
go

Thank you in advance!

Best,
Lishan

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