AMBER Archive (2007)

Subject: Re: AMBER: Nucleic acid analyse : base pair parameters, backbone torsions...

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Mon Jun 04 2007 - 17:00:25 CDT

ptraj is able to process trajectories of DNA simulations.

>- the average backbone torsions
you could either determine an average pdb structure of DNA for a certain time interval of the simulation using the "average" command of ptraj and measure the torsions yourself or get a list of torsion angles through the trajectory using the "dihedral" command of ptraj and plot the torsions on mgrace

>- the average base pair parameters
define donor / acceptor for base pairs in ptraj input
and run ptraj through the trajectory to determine h-bond occupancies between the base pairs..

> - the average pair step parameters
I guess i did not quite understand this one..could you give more details on what you are trying to accomplish here?

>- the average puckers
use the "pucker" function in ptraj input and run ptraj through the trajectory.
i.e., your pucker could be for C1' C2' C3' C4' forming a pseudodihedral angle across from O4' on each sugar ring.

hope this help..

regards,

jenk

   Cenk Andac, M.S., Ph.D. Student
 
 School of Pharmacy at
 Gazi University-Ankara Turkiye
 
  
  Address: Bandirma Sok. No:6
 
 Etiler, Ankara, 06330 Turkey
 
 Cell: +90-(536)-4813012
 
 E-Mail:cenk_andac_at_yahoo.com

       
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