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

[Mohammad Hassan Khatami]

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.
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
> 
> -- 
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
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> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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