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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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Tue Jun 19 2012 - 02:30:03 PDT
