Hello,
Please forgive me if this has already been addressed.
1. Can i use the vector function in amber (ptraj) to describe single or
double stranded oligonucleotide? (eg if i have a 10-mer ssDNA the
command can be vector A ':2-12')
2. is there a function in ptraj that can be used to define a plane by
using three atoms? (e.g. plane A ':1.x1' ':1.x2' ':1.x3')
3. Finally, can i calculate the angle between a vector and a plane (e.g.
Angle abc vectorA planeA outfile time)
a script can be written to calculate this for a specific coordinate,
there is a thread in 2007 by Ilyas Yildirim that discusses this. But i
really wish to get this angle calculated over a trajectory, preferably
using ptraj.
in the time correlation section of ptraj there is a vector command
defined by two atoms, can this command be extended?
e.g.
vector DNA :2-12.CA or vector DNA :2-12
plane SUR ':1.x1' ':1.x2' ':1.x3'
angle DNA SUR abc.dat time 10
Many thanks,
Taufik
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Apr 15 2010 - 10:30:02 PDT
