Hi Hannes,
Thanks for the clarification there, that makes a little more sense. There
are 72 LPS molecules in my system, so each atom supplied in the mask should
be present 72 times. The 0 one was a little harder to figure out, but your
comment put me on the right track. It turns out that the atom naming in my
prmtop is different than the atom names present in the original psf/pdb
combo that I used to create the prmtop. Some of the longer atom names
(H112R, H112S, etc) were truncated to 4 characters in the prmtop, which
explains why those masks evaluated to 0. If I supply the psf to cpptraj
instead of the prmtop, it runs without errors. Thank you for your
assistance!
On Thu, Apr 28, 2016 at 2:10 PM, <hannes.loeffler.stfc.ac.uk> wrote:
> 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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>
--
Amy Rice
Ph.D. Student
Physics Department
Illinois Institute of Technology
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Received on Thu Apr 28 2016 - 12:30:05 PDT
