RE: AMBER: Amber: xleap crash

From: Ross Walker <ross.rosswalker.co.uk>
Date: Fri, 13 Aug 2004 09:23:50 -0700

Hi Helios,
 
I have tried this out with xleap on Amber 8 and can confirm the same
problem. However, while xleap should not crash in the way it does the error
arrises because of problems reading the connectivity data at the end of the
pdb file. Xleap should ignore this data but in this case is not doing so.
This said you should really always clean up your pdb files before use.
Remove all the header information, connectivity data and anything else that
does not refer to an ATOM in your molecule. Insure you have the protonation
states of your residues correctly specified and that you have TER cards in
the correct place. Once I did this with your pdb xleap loaded it fine.
 
All the best
Ross
 
/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |



  _____

From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Helios
Sent: 13 August 2004 05:01
To: amber.scripps.edu
Subject: AMBER: Amber: xleap crash


Dear all, The xleap crash suddenly when I run 3dfr = loadpdb 3dfr.pdb. My
version is Amber7 and run at SGI system. The modified 3dfr.pdb is attached.




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Received on Fri Aug 13 2004 - 17:53:00 PDT
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