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 Mon Nov 16 2015 - 12:00:05 PST
