My protein is 476 residues. I would like to plot the map only for specific regions and mention it in the input thus choosing the residues i wish to calculate the contacts for. Does anyone know of any server /standalone programs for same?
Hi,
You can try Pymol. For further assistance you can view the discussion on research gate at ;
https://www.researchgate.net/post/Could_any_one_help_me_in_generating_a_residue-residue_contact_map
Regards
Or maybe, write a simple Perl script. It should be very easy to parse a pdb file to accomplish such task, I suppose...
Use the radius tool available in SPDBV. It will display the region falling in selected radius only. Further you can save a PDB file of displayed residues or a JPG also.
for finding the contact between the ligand and protein,can use Ligplot(stand-alone software)..
Note that pdbsum works only on deposited structures (ie the RCSB ones)
and how to generate protein-ligand heavy atom contacts using Gromacs? gmx mdmat.
Hello Revathi Sanker, there is a tool in VMD for this called Contact Map Plugin. Please check the link below:
https://www.ks.uiuc.edu/Research/vmd/plugins/contactmap/
However, this would only work for fully-atomistic representations. If this does not work, you may write a program to calculate the distances between the C-alpha atoms of the amino acid residues of interest. You would need to provide the three-dimensional coordinates of those C-alpha atoms as input. These are usually found in the PDB (NAMD)/GRO (GROMACS)/Dump (LAMMPS) file output of the simulation trajectory.
Most programs would not be able to read binary data, such as the DCD file of NAMD. Hence make sure your input file is in ASCII format i.e. readable using a text-editor.
Best of luck!
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