VMD-L Mailing List

From: Akshay Bhatnagar (akshaybhatnagar2790_at_gmail.com)
Date: Wed Nov 04 2015 - 23:46:02 CST

Hello everyone

I have around 5600 pdb files downloaded from rcsb.org. I want to generate
psf for all these files. For this i have already made a tcl script. But the
psf generation stops whenever it encounters a pdb files that contains an
amino acid other than the 20 essential amino acids. These amino acids are
generally the post translation modified amino acids. I tried removing them
using a perl scipt where i searched for pdb files that contain only 20
essential amino acid and HOH, but this has resulted in only 2 pdb files (it
is removing all the pdb files that contains ligands and drug molecules
also). I want to know is there any identifier through which i can remove
only the post translated modified amino acids.

With Regards
Akshay Bhatnagar
PhD Student
BITS Pilani Hyderabad Campus