AMBER Archive (2009)

Subject: [AMBER] Saccharides chains termini

From: Sergey Samsonov (
Date: Tue Jun 30 2009 - 09:32:53 CDT


I have the following question: when one creates a chain made up of
saccharide monomers, it is common that the terminal residue has 0 as a
first character in residue identifier, meaning that there is no more
open valences to continue the chain. What is about another terminus of a
saccharide chain? Though, for example, sequence {4GB 0GB} yields a
structure with a possibility to create the topology and coordinates
files without problems, there is C1 atom in the residue 4GB, which is
connected to O, C2 and a hydrogen (only three atoms, while C1 is
sp3-hybridized). Chemically it would be logical to add OH-group to this
C1-atom. Do you think it would be the proper way to proceed? And what
charges should I use then for the atoms C1, corresponding oxygen and
hydrogen of OH-group?

Thank you very much and best regards,


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