VMD-L Mailing List

From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Thu Nov 05 2015 - 16:28:31 CST

Hi Akshay,

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.

Cheers,

Tristan

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
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: Query for eliminating proteins with unusual amino acids

Hello everyone
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.


With Regards
Akshay Bhatnagar
PhD Student
BITS Pilani Hyderabad Campus