[AMBER] xleap facility to insert a residue

From: Sergey Samsonov <sergeys.biotec.tu-dresden.de>
Date: Fri, 24 Jul 2009 14:07:27 +0100


I'm facing the followign problem:

I have a complex of a protein and a saccharide in PDB file. There is TER
between a protein and a saccharide parts and consecutive numbering of
the residues. When I read this file with loadpdb everything is fine
except for the absence of OH-group on the 'left' end of the saccharide.
What commands should I use in xleap to add ROH residue on the left side
in this situattion? It works when I do something like y=sequence {ROH
x}, where x is an initial unit only if it contains only saccharide. I
tried to set a head atom to the atom I want to connect ROH on the
saccharide and then it also worked but the saccharide changed the
coordinates a lot relatively to the protein part.

It is not crucial and I found how to solve it (I can just add OH-group
by hand, specifying charges and types as they are defined in ROH residue
or I can preprocess the file to include ROH before reading in xleap) but
I'm almost sure that there is another, more elegant way, which is alos
less 'manual'.

Thank you very much in advance!

Best regards,


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Received on Fri Jul 24 2009 - 10:08:58 PDT
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