I generated a large number of peptide structures for a given sequence using the peptide builder module. However, the peptide builder module does not include hydrogen atoms all along the peptides. Is there any method through which I can add hydrogens to peptides ?
Sambit Kumar Mishra
There are some options to address your problem. I found this thread on stack exchange that might be useful - https://bioinformatics.stackexchange.com/questions/17916/how-can-i-programmatically-add-hydrogen-to-a-pdb-structure-using-biopython.
Besides, you can always use the Pymol GUI to add hydrogen atoms, particularly when you have a few proteins. Another software that can add hydrogen atoms is the SCWRL tool from the Dunbrack lab (http://dunbrack.fccc.edu/lab/scwrl).
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