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
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Received on Fri Nov 15 2013 - 21:00:02 PST
