RE: about dials_and_windows

From: Guanglei Cui <>
Date: Mon 2 Apr 2001 09:34:24 -0400

   I doubt that D&W can work well for your triplex structure. In the command
script, D&W specifies the sequence of one strand of your DNA and relies on
the complementarity. It may get confused by your 3-strand DNA. I think it
might work if you save the trajectory of each strand in a seperate file and
use D&W to analyze it (setenv numberofstrand 1). However, this will lose
some intrestrand information for sure.

Guanglei Cui

-----Original Message-----
From: thenmalar rathinavelan []
Sent: Monday, April 02, 2001 8:14 AM
Subject: about dials_and_windows

Hello ambers!
   I want to do analysis for my dna triplex molecule
using dials_and_windows. For that I used the following

setenv dna_or_protein dna
setenv sequence "CCCGGGGGCCCGGG" #sequence of the
first strand
setenv do_plotting yes
setenv include_first yes
setenv xrf_messages no
setenv coord_format pdb
setenv additional_file_format "Dynamics"
setenv start_time "0.0"
setenv time_interval "1.0"
setenv frequency "1"
setenv number_of_strands "2" #for the WC baseparis
of the triplex
setenv nucleotide "14"
setenv number_of_rows 14
setenv draw_dials yes
setenv draw_junction yes
setenv draw_helics yes
setenv device post
setenv constant_pressure yes
setenv molecular_topology_file_format amber
setenv molecular_topology_file ""
setenv skip_coordinate_set "0"
setenv stop_coordinate_set 20
setenv selections_file " "
setenv for007 "ST12dynPme.pdb” # pdb file got from
setenv for008 "ST13dynPme.crd" #trajectory file from

But it didn’t get any *.ps files (for dials and
windows). Also I am getting the following message

  Strand: 1 Unit: 1 (C 1) linkage from atom C1'
( 9) to C2' absent

Also, the output files are incomplete. For ex., part
of the base.out file is like the following:
Base Pair: C 1- G 28
                         Intra-Base Pair Parameters

     Config # SHR STR STG BKL

        1 1.75 4.49 -6.57 -15.59
  -2.62 -65.78
        2 1.38 2.02 -7.01 2.06
  -4.29 -72.84

          I will be very much thankful to you if
anybody help me to rectify this problem.
Thank you in advance.


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Received on Mon Apr 02 2001 - 06:34:24 PDT
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