I have 1000 pdb files. I want add polar hydrogen in the files. Could someone suggest any command line program to add polar hydrogens to pdb files?
SCWRL (http://dunbrack.fccc.edu/scwrl4/) should do that it no time. While the program is for mainly side-chain optimization, you can easily force it to freeze the coordinates of residues, by putting sequence in small letters.
Here what you need!
http://kinemage.biochem.duke.edu/software/reduce.php
Reduce is a program for adding hydrogens to a Protein DataBank (PDB) molecular structure file. Hydrogens are added in standardized geometry with optimization of the orientations of OH, SH, NH3+, Met methyls, Asn and Gln sidechain amides, and His rings. Both proteins and nucleic acids can be processed. HET groups can also be processed as long as the atom connectivity is provided.
Thanks, I tried the program but it is adding both the polar and non-polar hydrogens together. Is there any way to costomize it only for polar hydrogens? I could not find the option.
I have a related question. Is there a free Web-based (not command line) tool to add Hydrogen to a specific atom of a residue. For example, to add H atom to OD2 atom of an aspartic acid residue?
Thanks
If you have Python (2.7) and Chimera installed you can do the steps below.
1) Save a text file of the list of .pdb files you wish to edit, as pdblist.txt
2) Save the attached Python code as addph.py
3) Make sure the 2 files above, and the .pdb files to be edited are in the directory where you will run the commands
4) In command line, type the command below, which should generate a script.com file;
pathto/python addph.py pdblist.txt
5) Now, again in command line, type;
pathto/chimera --nogui script.com
This will use Chimera to edit each pdb file step by step. Wait until all the files are edited.
Hi, Ashmit Singh
you can use Mgltools (ADtools), which is a program for preparing ligands and receptors for docking. In it, you have the option of adding polar hydrogens.
Best Regards,
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