- Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ]

From: Taufik Al-Sarraj <taufik.alsarraj.utoronto.ca>

Date: Thu, 15 Apr 2010 13:04:14 -0400

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

Date: Thu, 15 Apr 2010 13:04:14 -0400

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

Custom Search