STANDALONE VERSION

NUPARM 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.

Click here to download NUPARM source code.

Additionally,if 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.

Click here to download BPFIND source code.

Note:

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


INSTALLATION:

      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.

  • nuparm2-2.f
  • parameters.h
  • coordinates.h
  • AdeVariants.name
  • CytVariants.name
  • GuaVariants.name
  • UraVariants.name

    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.

user@localuser:$ gfortran nuparm2-2.f -o nuparm2-2.exe


PROGRAM USAGE:

i) Direct

nuparm2-2.exe  <option>  <filename.pdb>

Options:

       -notdouble [default=double]
     (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)
     -ww [default=No]
              (to consider all base pairs as Watson-Crick type)
           -bpinf
        (Ouput file of BPFIND program)
           -overlap [default=No]
                (to calculate base pair stacking overlap between successive base pairs)

e.g:

user@localuser:$./nuparm2.2.exe 1BNA.pdb -pp -torsion  -single

ii) In combination with BPFIND

Run BPFIND on the PDB.

e.g: 

user@localuser:$./bpfind.exe -OL 1BNA.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)
    -VA [value] to set default pseudo angle cutoff (default = 120.0˚ )
    -EN [value] to set default E-value cutoff (default = 1.8 )
    -HT to include HETATM entries in PDB
    -CH to avoid identification of base pairs stabilized by C-H...O/N H-bonds
    -SG to avoid identification of base pairs involving sugar O2' atoms
    -AB to avoid base pairing between residue no. i and i+1
    -OL to avoid printing base pairing information w.r.t.the second strand.  This is suitable for simple oligonucleotides.

The output NUP and COR file are then used to run NUPARM.

user@localuser:$./nuparm2.2.exe -bpinf 1BNA.nup -pp -torsion 1BNA.cor

ii) MD trajectory analysis

user@localuser:$./nuparm2.2.exe <option> -trj <trj_file_name> -param NAME  -output <output_file_name>

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.