[AMBER] Few queries about simulation of protein - carbohydrate system

From: anu chandra <anu80125.gmail.com>
Date: Wed, 11 Nov 2015 12:59:07 +0000

Dear Amber users,

I am setting up a protein - carbohydrate (heparin) system for simulation
using Amber package. In this situation, I will be grateful to you if you
could help me to clarify few of my queries with setting up a
protein-carbohydrate system.

1. Based on literature, I think of using ff14SB as force-filed for protein
part. I have noticed that Amber (Amber14 Tools) contains two different
Glycam06 parameters, GLYCAM_06EPb and GLYCAM_06j-1. Which force filed will
better suit for this simulation?

2. Do I need to do any geometry optimization and partial atomic charge
calculation for the carbohydrate moiety (here heparin), as we do for
non-protein ligands? The paper here mentioned such a method,

3. Do I need to rename the atom names in heparin in order to match the one
present it Amber GLYCAM force filed (leaprc.GLYCAM_06EPb and

Many thanks in advance

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Received on Wed Nov 11 2015 - 05:00:05 PST
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