Hi,
This will work in CPPTRAJ if you use the same input (without the 'corr'
keyword, which is deprecated).
-Dan
On Friday, November 15, 2013, Indrajit Deb wrote:
> Dear AMBER users,
>
> I want to calculate the angle between two vectors.
>
> Vector1 will be between a pair of atoms and vector2 will between another
> pair of atoms.
>
> I tried to dump the vector1 and vector2 by the following command. But no
> output was written. The log is given here. The log saying output of corr no
> longer supported.
>
> I used that command according to the mailing list:
> http://archive.ambermd.org/200610/0180.html
>
> PTRAJ: trajin prodrun1.mdcrd
> Checking coordinates: prodrun1.mdcrd
> Rank: 0 Atoms: 3139 FrameSize: 76303 TitleSize: 81 NumBox: 3 Seekable 1
>
> PTRAJ: vector a1 :1.N9 corr :1.N1 out vec
> Mask [:1.N9] represents 1 atoms
> Mask [:1.N1] represents 1 atoms
> [No output trajectory specified (trajout)]
> prodrun1.mdcrd: 2000 frames.
>
> PTRAJ: Successfully read the input file.
> Coordinate processing will occur on 2000 frames.
> Summary of I/O and actions follows:
>
> INPUT COORDINATE FILES
> File (prodrun1.mdcrd) is an AMBER trajectory (with box info) with 2000
> sets
>
> NO OUTPUT COORDINATE FILE WAS SPECIFIED
>
> ACTIONS
> 1> VECTOR: storage to array named a1
> Calculate the vector between the center of mass of the two atom
> selections
> which follow (with the origin at the center of mass of the first)
> Atom selection 1 is :1.N9
> Atom selection 2 is :1.N1
> The order of Legendre polynomials is 2
> Warning: Output of corr, ired, corrired or corrplane vectors is not
> yet supported!
>
>
> How to save the vector1 and vector2 in a output file so that I can use
> these files for dot product between them to get the angles ?
>
> Is there any option to save Cartesian coordinates of any atom of my choice
> from the trajectory so that I can use any external program to carry out
> vector operations ?
>
> It will be very helpful if anyone suggest.
>
> -----indra
>
>
>
>
>
>
> ---------------------------------------------------------------------
> Indrajit Deb
> Kolkata, India.
> Mob: +919239202278
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org <javascript:;>
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Sun Nov 17 2013 - 09:30:12 PST
