I think he needs the GlcpNS prep files, not IdoA.


On Thu, Dec 3, 2015 at 10:20 AM, Arunima Singh <[log in to unmask]> wrote:
> Hi Anu,
>
> I gather you need to build a complex with a heparin tetrasaccharide
> containing Iduronic acids.  The prep files for the Iduronic acid residues
> are with various attachment points are in the attached file.  The naming
> currently uses a 4 letter residue name, where 2uA residue for example is the
> iduronic acid that allows a sulfate to be attached at the 2-O position. The
> numbers following this, 1, 2 or 3, allow using different conformations of
> IdoA where 1 = 1C4, 2 = 2SO and 3 = 4C1 conformation.  Please let me know if
> this works for you.  Let me know if there's any other prep file you need, or
> if you run into any problems.
>
> Regards,
> Arunima
>
> On Tue, Nov 17, 2015 at 8:47 AM, <[log in to unmask]> wrote:
>>
>> Hi Anu,
>> We have a new set of parameters and prep files for GAGs. Arunima, please
>> forward the files or links to Anu.
>> Thanks,
>> Rob
>>
>> Excuse the brevity, sent from iPhone
>>
>> On Nov 17, 2015, at 8:28 AM, anu chandra <[log in to unmask]> wrote:
>>
>> Hi Oliver,
>>
>>
>> Thanks for your prompt reply. A quick query here is about the RESP charge
>> calculation. I have noticed that in Glycam, the atomic partial charges are
>> derived for monosaccharide units and also mentioned about change in charge
>> while adding functional groups like sulfates. Do I need to do any  geometry
>> optimization and partial charge calculation for the heparin I am using?. The
>> heparin contains two disaccharide units.
>>
>>
>> Many thanks
>>
>> Anu
>>
>> On Mon, Nov 16, 2015 at 6:40 PM, Oliver Grant <[log in to unmask]>
>> wrote:
>>>
>>> Hi Anu,
>>>
>>> I forgot about adding sulfates. You'll also have to follow this page:
>>>
>>> http://glycam.org/docs/help/2014/04/04/adding-chemical-derivatives-to-glycam-residues/
>>>
>>> Oliver
>>>
>>> On Mon, Nov 16, 2015 at 6:12 PM, Oliver Grant <[log in to unmask]>
>>> wrote:
>>>>
>>>> Hi Anu,
>>>>
>>>> I think this is the standard protocol right now:
>>>>
>>>> Add these lines to your tleap input file. Insert your own paths and
>>>> forcefields that you are using.
>>>>
>>>> source /programs/amber/dat/leap/cmd/leaprc.GLYCAM_06j-1
>>>> source /programs/amber/dat/leap/cmd/leaprc.ff14SB
>>>>
>>>> You can see I'm using AMBER14. Now the hard part is getting your ligand
>>>> named correctly so that the correct GLYCAM parameters get assigned when you
>>>> load it into tleap. Protein residues have standard names in the PDB, but
>>>> unfortunately carbs do not. I assume you have a PDB format file of the
>>>> co-complex. You have to manually edit the PDB file with a text editor,
>>>> renaming the residues and atom names to GLYCAM nomenclature. See here for
>>>> the nomenclature to use: http://glycam.org/docs/forcefield/glycam-naming-2/
>>>> If this is your first time, it will be useful for you to build the sugar
>>>> on our website, download the PDB file, and open it up in a text editor. You
>>>> will see what format the carbohydrate residues and atom names need to be in.
>>>> Arunima Singh and others from the group have made a GAG builder for this:
>>>> http://glycam.org/tools/molecular-dynamics/oligosaccharide-builder/build-glycan?id=8.
>>>> Write back if you have any trouble with it. User feedback is precious to us.
>>>>
>>>> In the very near future (we are testing the software right now) we'll be
>>>> releasing software that renames everything for you, so this will be so much
>>>> easier.
>>>>
>>>> All the best,
>>>>
>>>> Oliver
>>>>
>>>> On Mon, Nov 16, 2015 at 3:35 PM, SUBSCRIBE GLYCAM-L Anu
>>>> <[log in to unmask]> wrote:
>>>>>
>>>>> Hello Glycam users,
>>>>>
>>>>> I am planning to do MD simulation of a protein-ligand complex in which
>>>>> ligand is heparin, made of 2-O-sulfo-aplha-L-iduronic acid and
>>>>> 2-deoxy-2-sulamido-alpha-D-glucopyranosyl-6-O-sulfate. I am using Amber 12
>>>>> MD package for simulation. It will be of great help if somebody can help me
>>>>> to get the Amber compatible Glycam  parameters for heparin.
>>>>>
>>>>>
>>>>> Many thanks
>>>>> Anu
>>>>
>>>>
>>>
>>
>
>
>
> --
> "You don't use science to show that you're right, you use science to become
> right."
>
> - Randall Munroe



-- 
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA