Hi,
I've never used the "vector" command in ptraj, but a brief look at the
manual explains why you get the following error (which is quite a useful
message anyway):
Error: vector: specified vector mode requires a second mask.
I presume you want to fit a plane through your lipids specified in the
first mask. The manual gives the following format for that:
vector name mask corrplane [out filename]
So in your case:
vector POPE :314-679 corrplane out pope.vector
(without corrplane, you'd need a second mask to define a vector)
Hope this helps,
Marc
On 19 June 2012 09:04, Albert <mailmd2011.gmail.com> wrote:
> hello:
> I am going to use ptraj vector command to analyze 'area/lipid' for
> the membrane system. here is my input file
>
> ------------
> /trajin md.mdcrd 1 50000 100
>
> vector POPE :314-679 out pope.vector /
> ------------
>
>
>
> PTRAJ: Processing input from file ptraj.in
> PTRAJ: trajin md.mdcrd 1 50000 100
> Checking coordinates: md.mdcrd
> Rank: 0 Atoms: 38394 FrameSize: 933000 TitleSize: 81 NumBox: 3 Seekable 1
> PTRAJ: vector POPE :314-679 out pope.vector
> Mask [:314-679] represents 15250 atoms
> Error: vector: specified vector mode requires a second mask.
> [No output trajectory specified (trajout)]
> md.mdcrd: 50000 frames.
> PTRAJ: Successfully read the input file.
> Coordinate processing will occur on 500 frames.
> Summary of I/O and actions follows:
> INPUT COORDINATE FILES
> File (md.mdcrd) is an AMBER trajectory (with box info) with 50000
> sets (processing only 500)
> NO OUTPUT COORDINATE FILE WAS SPECIFIED
> NO ACTIONS WERE SPECIFIED
> Processing AMBER trajectory file md.mdcrd
>
>
> thank you very much
> best
> Albert
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Received on Tue Jun 19 2012 - 01:30:03 PDT
