Thanks you very much for the reply Prof. Case.
On Fri, Nov 13, 2015 at 12:50 PM, David A Case <david.case.rutgers.edu>
wrote:
> 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
> instructions:
>
>
> http://glycam.org/docs/help/2014/04/04/adding-chemical-derivatives-to-glycam-residues/
>
> Look elsewhere on that site, or Google for "glycam sulfate" to get more
> information.
>
> >
> > 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)?
>
> Yes.
>
> ...good luck....dac
>
>
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Received on Fri Nov 13 2015 - 05:30:03 PST
