I think you can use MODELLER for missing residues and also Swiss PDB Viewer for missing atoms

https://salilab.org/modeller/

http://spdbv.vital-it.ch/

Yes, you need to reconstruct any missing atoms and/or residues. There are numerous programs that can do this. Do not use -missing with pdb2gmx; if you do, the topology is totally useless.

Thank you. Can you name one or two such programs which are open source ?

http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources

I think you can use MODELLER for missing residues and also Swiss PDB Viewer for missing atoms

https://salilab.org/modeller/

http://spdbv.vital-it.ch/

I do not perefer Swiss if one has many more missing residues. MODELLER is the best solution.

Now it having charge 5.add the missing amino acids/atoms

What study your going to perform with this structure?

Take the raw fasta format of the pdb and aligned it with the 3d coordinate of the pdb and generate random coordinate of the missing residue using modeller and perform md

Hi,

i-Tasser is a web-service to create even small portion of missing proteins. have look: http://zhanglab.ccmb.med.umich.edu/I-TASSER/

If you don't have many structures you can build it by hand. you can build the rotamers that YOU prefer and/or avoid clashes that are often generated by automated methods.

you can us Coot or UCSF Chimera for that - it's easy :)

http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/

http://www.cgl.ucsf.edu/chimera/

You can use the automodel script from modeller in order to complete the residues. Additionally you may use this server: http://lorentz.immstr.pasteur.fr/pdb/frozen_submission.php