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

[Justin Lemkul]

On 5/19/17 9:57 AM, Mohammad Hassan Khatami wrote:
> 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.
>

Linkages are not specific to the sugar; most are totally generic.  A few 
comments suggest specific usage and may be corner cases, but your patches will 
be among 14aa, 14ab, 14ba, 14bb.

>
> Then, I might need to branch them with1->6 linkage.

Also totally possible.

> I tried Glycan Reader, but itstill crashes.
>

Uploading a correctly named PDB file should work in Glycan Reader or the Quick 
MD Simulator, but "still crashes" is not diagnostic of anything.  Specific help 
with CHARMM-GUI should be brought to their attention, though.

-Justin

> 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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>

-- 
==================================================

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

==================================================