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

Mon May 22 12:46:12 CEST 2017

On 5/22/17 1:09 AM, Mohammad Hassan Khatami wrote:
> 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:

Note that your residue name must be limited to 4 characters so it can properly 
be read from the input coordinates.  AGLC14 won't work.

> ! 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
>

Correct.

> 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?

You should not do this.  The .vsd file is for defining virtual sites.  The IC 
lines are for the CHARMM program's internal coordinate builder, specifying some 
optimized geometry (one that the force field in total should produce, or come 
very close).  All the bonded parameters you need are already in the force field 
because they come from the corresponding .prm files.  Do not adjust bonded 
parameter files.

-Justin

>
> 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
>>>> http://mackerell.umaryland.edu/~jalemkul <http://mackerell.umaryland.edu/~jalemkul> <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
>>
>> ==================================================
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>> Gromacs Users mailing list
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>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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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

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