[AMBER] lipidorder in cpptraj

From: Chitrak Gupta <chgupta.mix.wvu.edu>
Date: Wed, 7 Feb 2018 19:13:59 -0500


I am trying to calculate lipid order parameter in cpptraj. I have two

1. What is the difference between the following two (I seem to get the
exact same output in both)

lipidorder out filename.dat scd ....(mask)...

lipidorder out filename.dat z scd ....(mask)....

2. Second, I am still a bit confused about the mask syntax. If I want to
select say C115 of PA chain of POPC, then should it be the following?

lipidorder out filename.dat scd ":PA.C115" ":PA.H15R" ":PA.H15S"

I saw previous posts where people used <dot> instead of . and ended up with
an empty output.....which also seems to happen to me. Just want to verify
which is the correct way.

Best regards,
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Received on Wed Feb 07 2018 - 16:30:02 PST
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