standalone version is GNU
Fortran code that can be compiled using the latest GFORTRAN compilers.
If you which to install the program, please read the instruction below.
here to download
NUPARM source code.
interested in getting Base pair information of the structure, use
BPFIND program. Its a fortran program that identifies basepairs details with classifications based on standard base-edges. It is mainly useful for analysing RNA
structures that contains Non-Waston-Crick basepairs. Output
of BPFIND can directly be passed to
NUPARM for geometric anlaysis of the structures.
here to download BPFIND source code.
Features and additionaly functionalities can be added on request. Please contact Prof. Dhananjay or Prof. Bansal with the request. The latest and beta versions of NUPARM and BPFIND can also be downloaded from http://www.saha.ac.in/biop/bioinformatics.html
The program is organized in a single Fortran program file with two header files. Uncompress "nuparm.tar.gz" file.
The folder "nuparm" contains the following files.
Program can be compiled by most of the available compilers, such as g77, g95, ifort, gfortran, etc. The program requires four files (AdeVariants.name, etc) containing names of different nucleotide variants. In the supplied code the program expects those files are place in /usr/local/bin directory. Please transfer the above files in /usr/local/bin before compiling the program. In case you do not have access to /usr/local/bin you may keep the files in any other directory, such as $HOME/bin, and modify the code (line no. 1024, 1033, 1041 and 1049) and compile again.
(Use this option when the Nucleic acid structure is not a double helical)
-notpdb [default=pdb format]
-lsfit [default=cross-product method]
-c1c1 [default=C6-C8 line as Y-axis]
-cg [default=C6-C8 midpoint as BP center]
-single [default=No Single Strand Parameter]
-orient "atom selection" [default=Not required]
(Usualy "C1' " atom is selected for reorienting the molecule)
-pp [default=Not required]
(Gives parameter calculated using Phosphate atom; Xp, Yp, Zp, Inter-chain P--P distances & intra-strand P--P distance)
-torsion [default=Not required]
(Gives Backbone, Glycosidic and sugar torsion angles)
(to consider all base pairs as Watson-Crick type)
(Ouput file of BPFIND program)
(to calculate base pair stacking overlap between successive base pairs)
combination with BPFIND
BPFIND on the PDB.
Details on how to run BPFIND is provided along with BPFIND source code.
The following options can be used:
-HD [value] to set default hydrogen bond distance cutoff (default = 3.8 Å)
The output NUP and COR file are then used to run NUPARM.
ii) MD trajectory analysis
where the parameter NAME can be any of the base pair parameters, such as propeller, buckle, etc, any of the base pair doublet parameters, such as Tilt, Roll, etc or any of the main chain torsion angle, such as Alpha, Beta, etc, Sugar pucker, phase, Interchain P...P distance (PP) and Zp.