RE: AMBER: Problem!!

From: Ross Walker <ross.rosswalker.co.uk>
Date: Mon, 19 Mar 2007 08:23:40 -0700

Dear Anju,
 
!FATAL ERROR----------------------------------------
!FATAL: In file [atom.c], line 444
!FATAL: Message: bondAtomProblem found

If you search the archive (http://amber.ch.ic.ac.uk/archive/) you will find
a large number of similar messages where people have across this problem and
in here are likely a number of fixes:
 
http://www.google.com/search?hl=en
<http://www.google.com/search?hl=en&domains=amber.ch.ic.ac.uk&q=Message%3A+b
ondAtomProblem+found&sitesearch=amber.ch.ic.ac.uk>
&domains=amber.ch.ic.ac.uk&q=Message%3A+bondAtomProblem+found&sitesearch=amb
er.ch.ic.ac.uk
 
I would also try stripping everything from the pdb file that is not
required. That is all the HEADER, REMARK etc fields as well as all the
connectivity information at the end of the file. Also make sure you have TER
cards in the correct places.
 
If that still doesn't fix the problem then please send your pdb file as an
attachment. It is very hard to debug things without being able to reproduce
exactly what you did.
 
Can you also please try to use more descriptive subject lines - this will
help improve the mailing list archive by allowing messages to be more easily
categorized.
 
All the best
Ross
 
/\
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|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
| http://www.rosswalker.co.uk <http://www.rosswalker.co.uk/> | PGP Key
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Received on Wed Mar 21 2007 - 06:07:18 PDT
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