From: Shirley Hui (shirleyhui_at_alumni.uwaterloo.ca)
Date: Mon Dec 20 2004 - 21:39:30 CST
MessageDeleteing the hydrogens and letting psfgen guess them worked!
Thanks Blake,
shirley
----- Original Message -----
From: Blake Charlebois
To: namd-l_at_ks.uiuc.edu
Sent: Monday, December 20, 2004 8:27 PM
Subject: RE: namd-l: Failed to set coordinate for atom errors!
Hi Shirley,
It looks as though your PDB file and your topology file have different naming conventions for hydrogen atoms. Have you tried deleting all hydrogen atoms and letting psfgen guess the correct coordinates? Many people recommend this. http://www.ks.uiuc.edu/Research/namd/tutorial/PSC2001/pdf/NAMDassembly.pdf
You can also alias the hydrogen atoms or manually change their names in the PDB file. You can find naming conventions at http://www.bmrb.wisc.edu/ref_info/atom_nom.tbl and in the topology file.
Blake
-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf Of Shirley Hui
Sent: December 20, 2004 5:32 PM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: Failed to set coordinate for atom errors!
Below are the files I am using to run psfgen with:
PDB
http://www.bioinformatics.uwaterloo.ca/~s2hui/6paxOrig.pdb
PSFGEN.IN file
http://www.bioinformatics.uwaterloo.ca/~s2hui/psfgen.in
TOPOLOGY file
http://www.bioinformatics.uwaterloo.ca/~s2hui/top_all27_prot_lipidinp
and the errors I see are:
http://www.bioinformatics.uwaterloo.ca/~s2hui/psfgen.out
I was wondering how to get rid of the:
"Warning: failed to set coordinate for atom..." errors??
Thanks
shirley
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