RE: Failed to set coordinate for atom errors!

From: Blake Charlebois (bdc_at_mie.utoronto.ca)
Date: Mon Dec 20 2004 - 19:27:51 CST

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
<http://www.bioinformatics.uwaterloo.ca/~s2hui/top_all27_prot_lipid.inp>

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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