From: Lekpa Duukori <duukori.gmail.com>
Date: Wed, 24 Mar 2010 16:43:32 -0600

Hi All,

I need some advice regarding FF parameters.

I have a molecule where a covalent bond exists between a peptiod and a
sugar. Parameters exist in AMBER and GLYCAM respectively for each but due to
scaling (dihedral rotamer population is important in my work)issue with
SCEE and SCNB I have derived charges for the peptiod using the GLYCAM
approach ( ~200 structures from MD, CHelpG, 0.01 wt etc ). This is
relatively easy as my system is small. MD using the new charges ( without
SCEE/SCNB scaling of course and using AMBER valence parameters ) yield very
similar structures (rsmd) in solution as model using parm99SB charges.

I am thinking this is probably fine but I would like people's opinion!


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Received on Wed Mar 24 2010 - 16:00:04 PDT
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