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

From: David A Case <>
Date: Fri, 13 Nov 2015 07:50:14 -0500

On Wed, Nov 11, 2015, anu chandra wrote:
> 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?

You should use GLYCAM_06j-1, but you will need to do some extra prep work to
create the sulfate modifications that you need. Here is a page of

Look elsewhere on that site, or Google for "glycam sulfate" to get more

> 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
> leaprc.GLYCAM_06j-1)?


...good luck....dac

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Received on Fri Nov 13 2015 - 05:00:03 PST
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