From owner-chemistry@ccl.net Thu Aug 11 04:52:01 2011
From: "Gonzalo Jimenez Oses gonzalo.jimenez(a)unirioja.es" <owner-chemistry _ server.ccl.net>
To: CCL
Subject: CCL: Residue annotation in MOZYME
Message-Id: <-45239-110811044953-25365-rJgIw2zR/3KJ03w7m2ylcQ _ server.ccl.net>
X-Original-From: "Gonzalo  Jimenez Oses" <gonzalo.jimenez**unirioja.es>
Date: Thu, 11 Aug 2011 04:49:50 -0400


Sent to CCL by: "Gonzalo  Jimenez Oses" [gonzalo.jimenez^-^unirioja.es]
Dear all,

I have observed that MOPAC overrides the residue labels specified in the PDB 
files when they are used as inputs for MOZYME. For example, a Pro can be 
automatically changed into a Val after reading the PDB input. This has terrible 
consequences for the global charge computation. Of course, one can fix the 
carge manually, but this is not very convenient when processing dozens of PDB 
files in batch mode.

The cause of these changes is very slight deviations from the "ideal" residue 
geometry (I have overriden this bug by just changing the XYZ coordinates of 
just one atom of the conflictive Pro).
So, my question is: given that the residue labels are already specified in the 
PDB file, is there any way to override the automatic re-tagging of the residues 
before any MOZYME calculation?
I have checked the documentation, but have not found anything.

Thanks a lot, best regards,

Gonzalo