Thanks for your valuable and helpful reply, Prof. Case and Lachele.
On Mon, Nov 16, 2015 at 7:40 PM, Lachele Foley <lf.list.gmail.com> wrote:
> Sorry not to reply sooner. What Dave said is good. Also, I see that
> you wrote to, and got other good information from, the GLYCAM-L list
> (ref below for people with interest). I would only add that the
> geometry you would get from the GAG builder or the Carbohydrate
> Builder should be a good starting geometry. Of course, you will need
> to go through the usual minimization and such for the complete system.
> But, the initial geometry of the glycan should be ok for starting the
> simulation. Of course, if you already have a starting geometry (from
> experiment, for example), then using that is fine.
>
> Link to thread on other list:
> https://listserv.uga.edu/cgi-bin/wa?A2=GLYCAM-L;ee8be00f.1511
> GAG Builder shortcut URL: glycam.org/gag
> Carbohydrate Builder shortcut URL: glycam.org/cb
>
>
> On Fri, Nov 13, 2015 at 8:20 AM, aneesh cna <aneeshcna.gmail.com> wrote:
> > 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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> >>
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>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
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Received on Tue Nov 17 2015 - 06:00:03 PST
