Of course, your input must be one logical line. So unless your masks are not on a single line you would have to put a backslash at the end of every one (except the last one).
________________________________________
From: Amy Rice [arice3.hawk.iit.edu]
Sent: 28 April 2016 19:30
To: amber.ambermd.org
Subject: [AMBER] Cpptraj LipidOrder error: mask groups are not the same length
Hi all,
I have a lipopolysaccharide bilayer system (36 LPS per leaflet) that I have
simulated for 750 ns; I am now trying to calculate order parameters (Scd)
for the 6 LPS acyl chains. I tested LipidOrder first on a DPPE bilayer
system, and cpptraj calculated Scd without error. However, when I used the
exact same command for one of the acyl chains of the LPS system (after
changing the atom mask to the appropriate atom names), I received the
following error: "OrderParameter: mask groups are not the same length (0
72)". I have pasted the command I used below. The prmtop and sample
trajectory are too large to be included with this email, but I am very
happy to send them off list. I am using AmberTools 15.
lipidorder out chain1.dat z scd \
":LIPA.C12" ":LIPA.H12R" ":LIPA.H12S" ":LIPA.C13" ":LIPA.H13R" ":LIPA.H13S"
":LIPA.C14" ":LIPA.H14R" ":LIPA.H14S" ":LIPA.C15" ":LIPA.H15R" ":LIPA.H15S"
":LIPA.C16" ":LIPA.H16R" ":LIPA.H16S" ":LIPA.C17" ":LIPA.H17R" ":LIPA.H17S"
":LIPA.C18" ":LIPA.H18R" ":LIPA.H18S" ":LIPA.C19" ":LIPA.H19R" ":LIPA.H19S"
":LIPA.C110" ":LIPA.H110R" ":LIPA.H110S" ":LIPA.C111" ":LIPA.H111R"
":LIPA.H111S" ":LIPA.C112" ":LIPA.H112R" ":LIPA.H112S" ":LIPA.C113"
":LIPA.H113R" ":LIPA.H113S"
Any help or recommendations would be greatly appreciated!
Thank you,
- Amy
--
Amy Rice
Ph.D. Student
Physics Department
Illinois Institute of Technology
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Received on Thu Apr 28 2016 - 12:30:04 PDT
