____ _ _ _ _ _______ _ _ _ _
| _ \ | \ | | /\ | | | | | ___ | | | | | \ \ / /
| | \ \ | |\ | | \ \ | | | | | | \| | | | | \ \ / /
| | | | | | \ | | / \ \ | |___| | | |__ | | | | \ \/ /
| |_/ / | | \ | | / / \ \ | |___| | | __| | | | | \ \/
| _ / | | \ | | / /___\ \ | | | | | | | | | | / \ \
| | \ \ | | \| | / /_____\ \ | | | | | |___/| | |____/| | | / / \ \
|_| \_\ |_| \_|/ / \_\ |_| |_| |______| |_______| |_| /_/ \_\
=================================================================================== -----=====%-+-+-+%=====-----
- Bhattacharyya,D., Halder,S., Basu,S., Mukherjee,D., Kumar,P. and Bansal,M. (2017) RNAHelix: computational modeling of nucleic acid structures with Watson–Crick and noncanonical base pairs. J. Comput. Aided. Mol. Des., 31, 219–235.
-
S. Mukherjee, M. Bansal and D. Bhattacharyya (2006) Conformational specificity of non-canonical base pairs 4 and higher order structures in nucleic acids: crystal 5 structure database analysis, J. Comp. Aided Mol. Des. 20, 629-45.
-
Bansal,M., Bhattacharyya,D. and Ravi,B. (1995) NUPARM and NUCGEN: software for analysis and generation of sequence dependent nucleic acid structures. Comput. Appl. Biosci., 11, 281-287.
-----=====%-+-+-+%=====-----
|>RNAHelix
|
--DataSet.dat
|
--prm2param.pl
|
--parameter.loc
|
--RNAHelix.f
|
--RNAHelix.exe
|
--RNAHelix.linux
|
--par_all27_na.inp
|
--top_all27_rna.inp
|
--top_all27_dna.inp
|
--minimize.inp
|
--README
|
--LICENSE
|
--sample/
If you do not receive all the files mentiond above then there is some problem Download the.tar again to run it properly.
-----=====%-+-+-+%=====-----
G77 compiler or Intel ifort compiler is required for running the programme.
-----=====%-+-+-+%=====-----
Installation Linux 
- Global:
The precompiled version requires the file "DataSet.dat" to be placed in
/usr/local/bin . In case you are unable to copy the supplied DataSet.dat
file into /usr/local/bin, please modify the source-code (line no. 687) to
specify the correct location of the file and recompile using a suitable
FORTRAN-77 compiler. -----
For local installation just put the uncompressed file in desired location
and run the software from any where using the full path or you can add the
folder location to your PATH variable.
if you have put your folder in /home/Username/bin/RnaHelix, for example,
then
bash:
PATH=$PATH:/home/Username/bin/RnaHelix
export PATH
tcsh:
setenv PATH $PATH\:/home/Username/bin/RnaHelix -----=====%-+-+-+%=====-----
./RNAHelix.g77
Input [mandatory] Description
-------------------------------------------------------------------------------
DataSet.dat ideal parameter files for nucleotides with
Watson-Crick, Sugar and Hoogsteeien edges this
file is important for the generation of nucleotides
parameter.loc rotational, translational and vibrational
parameters to be used for the generation of
nucleic acid structure. This file is prepared
by processing the nuparm output *.prm with prm2param.pl
Output [default] Description
-------------------------------------------------------------------------------
allatoms.pdb the regenerated nucleotide structure file in .pdb
format
centers.bpc basepair centers
double.hlx basepairing information of the regenarated helix -----=====%-+-+-+%=====-----
DataSetSugar.dat
<><><><><><><><>
this file is segmented into 15 segments (four nucleotides[ACGT/U] with all
three edge of binding Watson-Crick, Sugar, and Hoosteeine). It contains the
ideal parameters for helix generation and, therefore, SHOULD NOT BE MODIFIED.
parameter.loc
<><><><><><><>
1st line
---------------
col 1-4 int number of base-pair
col 8 0/1 0 for no sequence file and 1 for using sequence file
col 12
col 16- name of the prm file used for generation
subsequent lines
-----------------
col 1-3 nucleotide information
col 5-8 basepairing type
col 13-18 Tilt
col 21-26 Roll
col 29-34 Twist
col 37-42 Shift
col 45-50 Slide
col 53-58 Rise
col 61-66 Buckle
col 69-74 Open
col 77-82 Propel
col 85-90 Stagger
col 93-98 Shear
col 101-106 Stretch
Tilt Roll Twist Shift Slide Rise Buckle Open Propel Stagger Shear Stretch
C:G W:WC -0.34 5.69 29.18 0.20 -2.09 3.30 6.15 -1.10 -5.85 -0.03 0.31 2.94
allatoms.pdb
<><><><><><>
this file is the primary output of the RnaHelixGen software. this file is is
in format of pdb file. one can visualize the file in Pymol/Rasmol/VMD or any
standard visualizing tools.
centers.bpc
<><><><><>
double.hlx
<><><><><>
this file shows a textual visualization of the structure with cannonical and/or
non-cannonical basepairing information, where '|' stands for a Watson-Crick edge
pairing, '-' stands for Sugar edge pairing and '*' stands for Hoosteeine edge
pairing
Additional files for Backbone Generation by CHARMM
<><><><><><>
Please use one of the supplied topology files appropriate for your molecule.
Minimize the allatoms.pdb file using minimize.inp script, which reads the
sequence of the DNA/RNA from Sequence.str file.
<><><><><><>
We recommend use of BPFIND and NUPARM as additional data preparation tools.
These also can be downloaded from [Bioinformatics](http://www.saha.ac.in/biop/bioinformatics.html) page.