[gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides

[Mohammad Hassan Khatami]

First, I am looking for 1->4 and 1->6 linkages. In the top_all36_carb.rtf file I found different linkages for beta-glucose, but non for alpha-glucose.
I am trying to make a simple chain with 1->4 linkages like below:

alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose.


Then, I might need to branch them with1->6 linkage.
I tried Glycan Reader, but it still crashes.

MH
> 
>> Thanks Justin.
>> I have tried the CHARMM-GUI but it crashed. I might need to modify the order of the atoms in my PDB file, which I have created using GLYCAM-Web GUI. I have downloaded the “toppar_c36_feb16” but I did not find a manual on how to apply them (any suggestions?), so it did not go far.
> 
> What you need to do depends on linkages.  There are patches (PRES in CHARMM .rtf files) that tell you how each residue is manipulated in the case of a patch; refer to the CHARMM documentation online for specifics.  The file you'll need is top_all36_carb.rtf.
> 
> Otherwise, use the force field files as a template to rename your input structure so CHARMM-GUI can process it.  This is probably the much faster route.
> 
> -Justin
> 
>> I'll play with these two, and I'll be back.
>> MH
>>> On May 18, 2017, at 5:08 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>> 
>>> 
>>> 
>>> On 5/18/17 4:57 PM, Mohammad Hassan Khatami wrote:
>>>> Hi,
>>>> 
>>>> I am trying to run simulations on alpha-D-glucose polymers. I have done these simulations using AMBER and I am wondering if it is possible to run them employing CHARMM36 in GROMACS, as well?
>>>> It seams that CHARMM36 in GROMACS has only implemented monomers of alpha-D-glucose as ”AGLC”. Is there a way to introduce the whole polymer to the GROMACS?
>>>> 
>>> 
>>> Sure, you can treat it like any polymer, but you'll have to create the internal monomer residues yourself from the patches in the original CHARMM force field files.
>>> 
>>> Or try CHARMM-GUI; it should handle what you need and give you all the necessary GROMACS inputs.
>>> 
>>> -Justin
>>> 
>>> --
>>> ==================================================
>>> 
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>> 
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>> 
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
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>> 
> 
> -- 
> ==================================================
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalemkul at outerbanks.umaryland.edu <mailto:jalemkul at outerbanks.umaryland.edu> | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul <http://mackerell.umaryland.edu/~jalemkul>
> 
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