Hi,
I am a new user of Amber, so this may seem like a rather trivial question.
I am trying to build a polysaccharide that includes a KDO unit. According
to the AmberTools manual I have it appears that GLYCAM-06 should have
specifications for KDO in the GLYCAM-06.prep file. However when I search
for the residue code KO it comes up empty. So does anyone know where I
should look/have KDO prep files? I need one for a terminal beta-KDO and
one for a beta-KDO with a linkage in the 3 position. I have looked at the
most recent version of the GLYCAM-06.prep file online as well.
Also since KDO has a two letter code, how do I specify linkages and alpha
vs beta form in a three letter code?
Thanks,
Camille
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Received on Wed Feb 01 2012 - 17:30:05 PST
