rmsd

C program for calculating rmsd from a charmm DCD file.

Dependencies

Lapack and Blas are required for compiling this software.

How to run

Please provide 4 arguments to the program:

• path to CHARMM dcd file (binary)
• path to reference structure (CHARMM .cor text file)
• atoms selection for rmsd (command line)
• atoms selection for centering (command line)

Note that it is not necessary to use 2 identical selections for centering and rmsd

For a selection by residue name (3rd column of CHARRMM .cor file): ./rmsd *.dcd *.cor rmsd=resname:GLY,LEU center=resname:GLY,LEU

For a selection by atom name (4th column of CHARRMM .cor file) : ./rmsd *.dcd *.cor rmsd=atname:C,CA,N center=atname:C,CA,N

For a selection by residue number (2nd column of CHARMM .cor file) : ./rmsd *.dcd *.cor rmsd=resnum:15,19,62,101 center=resnum:15,19,63

For a selection by atom number (1st column of CHARMM .cor file) : ./rmsd *.dcd *.cor rmsd=atnum:1114,1123,1169,2056,6987 center=atname:C,CA,N