[gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides
Mohammad Hassan Khatami
mhk302 at mun.ca
Mon May 22 07:33:29 CEST 2017
Hi Justin,
I am asked to focus on learning how to change and update the CHARMM36 parameters, so I could implement the future changes and patches easier. (Thus, I am not focused in the Glycan Reader, at the moment.)
Thank you! I think I now have a better understanding of what should I do. For each part of my polymer,i.e. the initial, the middle and the final part, I have to modify the AGLC molecule to represent each of these parts, seperately.
So, lets say to introduce the 1->4 linkage, I need to to apply 14ba patch from the top_all36_carb.rtf into the merged.rtp file of GROMACS CHARMM36. In this case, I need to create a new version of [ AGLC ] molecule (lets call it [ AGLC14 ]) in the merged.rtp, with the changes below from the the top_all36_carb.rtf, applied to it:
! equatorial-axial 1->4 linkage
PRES 14ba 0.02 ! (i)1->4(i-1) equatorial at C1 and axial at C4
dele atom 1HO4
dele atom 2HO1
dele atom 2O1
ATOM 1C4 CC3161 0.09 !
ATOM 1O4 OC301 -0.36 !
ATOM 2C1 CC3162 0.29 !
BOND 1O4 2C1
I have to remove the HO4, HO1 and O1 lines and modify the values for the C4, O4 and C1 atoms. Then, I need to add the bond of
[ bond ]
…
O4 +C1
Then, I need to apply the bonds and angles parameters in the the top_all36_carb.rtf (below), into the merged.vsd file of the GROMACS CHARMM36.
! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL)
IC 1C3 1C4 1O4 2C1 1.5071 110.40 -86.30 121.00 1.3902 ! psi
IC 1C4 1O4 2C1 2O5 1.4560 121.00 -130.97 108.63 1.4470 ! phi
IC 2O5 1O4 *2C1 2C2 1.4470 108.63 -122.09 110.89 1.5316
IC 2O5 1O4 *2C1 2H1 1.4470 108.63 121.92 111.32 1.0837
I have figured out how to implement R(IK), T(IKJ), T(JKL) and R(KL) values into the merged.vsd file, except for the PHI values. Where (and/or how) should I put it?
Am I on the right track?
Thanks again for your help.
MH
> On May 19, 2017, at 5:36 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
>
> 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> <mailto:jalemkul at outerbanks.umaryland.edu <mailto:jalemkul at outerbanks.umaryland.edu>> | (410) 706-7441
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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
>
> ==================================================
> --
> Gromacs Users mailing list
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