Hi,
On Wed, Feb 7, 2018 at 7:13 PM, Chitrak Gupta <chgupta.mix.wvu.edu> wrote:
> 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)....
There is no difference because 'z' is the default axis (so you're
calculating w.r.t. 'z' in both cases).
> 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.
Yes, '.' is the correct symbol for "atom" in Amber mask parser syntax,
so I think the above should work.
Note that in the GitHub version of cpptraj there is another command
for calculating lipid order parameters with a simpler syntax called
'lipidscd' (syntax below). This command will automatically search for
lipid chains, is fully integrated into cpptraj's dataset/datafile
framework, and works with the MPI and/or OpenMP versions of the code.
The only current limitation is that it requires hydrogens present,
i.e. it won't work for united atom systems. If you get a chance to try
it I'd appreciate any feedback.
-Dan
> help lipidscd
[<name>] [<mask>] [{x|y|z}] [out <file>] [p2]
Calculate lipid order parameters SCD (|<P2>|) for lipid chains in mask
<mask>. Lipid chains are identified by carboxyl groups, i.e.
O-(C=O)-C1-...-CN, where C1 is the first carbon in the acyl chain
and CN is the last. Order parameters will be determined for each
hydrogen bonded to each carbon. If 'p2' is specified the raw <P2>
values will be reported.
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Thu Feb 08 2018 - 04:00:02 PST
