From: Sujata Sovani (
Date: Tue Sep 08 2009 - 17:47:43 CDT

Hi VMD USers,

I am new and following the NAMD tutorial for ubq.
I have a protein with ATP and acetylated N-term.

When I do
set xyz [atomselect top protein]
$xyz writepdb xyznew.pdb

ATP gets deleted (and so does ACE which is fine) but I need ATP.
When I do

set xyz [atomselect top all]
$xyz writepdb xyznew.pdb
ACE and ATP stay and then when I convert it to PSF file, I get a fatal error due to ACE. I can delete ACE from xyznew.pdb and proceed but if I do this something weird happens to my ATP and I get repeated errors when I run NAMD.

I want to know - is there a way to keep the hetatom ATP and remove ACE right at the first stage of writing pdb from the original pdb - in the atomselect command or thereafter?