Hi,
Are you using AmberTools12? (I looked in that manual).
If so, this is a question for those that develop ptraj and/or have used
vector for area/lipid before.
If not, try AmberTools12.
--Marc
On 19 June 2012 10:13, Albert <mailmd2011.gmail.com> wrote:
> Dear Marc:
> thank you very much for kind reply.
>
> it seems to work now. However, the log file claimed:
>
> Warning: Output of corr, ired, corrired or corrplane vectors is
> not yet supported!
>
>
> here is the full log files:
>
>
> PTRAJ: vector POPE :314-679 corrplane out pope.vector
> Mask [:314-679] represents 15250 atoms
> [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
>
> ACTIONS
> 1> VECTOR: storage to array named POPE
> Calculate the vector perpendicular to the least squares best plane
> through the atom selection which follows
> Atom selection is :314-679
> The order of Legendre polynomials is 2
> Warning: Output of corr, ired, corrired or corrplane vectors is
> not yet supported!
>
>
> Processing AMBER trajectory file md.mdcrd
>
> 1% ............ 25% ............ 50% ............ 75% ............ 100%
>
>
> PTRAJ: Successfully read in 500 sets and processed 500 sets.
>
> Dumping accumulated results (if any)
>
>
>
>
> On 06/19/2012 10:18 AM, Marc van der Kamp wrote:
> > 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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> >>
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>
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Received on Tue Jun 19 2012 - 03:00:02 PDT
