VMD-L Mailing List
From: Sujata Sovani (sujatas_at_scripps.edu)
Date: Tue Sep 08 2009 - 17:47:43 CDT
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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?
Thanks.
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- Reply: John Stone: "Re: How to select a hetatom while get rid of N-term ACE in atomselect"
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