VMD-L Mailing List
From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Thu Nov 05 2015 - 16:28:31 CST
Probably the easiest way to do this is to take advantage of the fact that, to VMD, “protein” is anything that contains atoms named C, N, CA and O – which should catch all non-standard amino acids as well. So if you do:
set sel [atomselect top protein]
set resnames [lsort –unique [$sel get resname]]
… then all you have to do from there is a simple check of $resnames against a list of standard amino acid resnames.
From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Akshay Bhatnagar
Sent: Thursday, 5 November 2015 3:46 PM
Subject: vmd-l: Query for eliminating proteins with unusual amino acids
I have around 5600 pdb files downloaded from rcsb.org<http://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.
BITS Pilani Hyderabad Campus