[gmx-users] Carbohydrate force fields in GROMACS

[Justin Lemkul]

On 3/20/15 1:16 PM, Marcelo Depólo wrote:
> As my previous email said: there is a modified GROMOS forcefield for
> carbohydrated. Install it and check out which kind of modifications on
> topologies you should do.
>

Install it, sure, but from where?  You provided a DOI to the article, which 
makes no reference to the availability of the parameters.  If the implication is 
that one needs to manually modify all of the force field files according to what 
the authors reported, that's one thing, but if you know of a site from which you 
can download the modified force field, that would be helpful.  I would be 
curious to see how well the parameters perform, as well.

-Justin

>
> 2015-03-20 13:51 GMT-03:00 Justin Lemkul <jalemkul at vt.edu>:
>
>>
>>
>> On 3/20/15 12:46 PM, mish wrote:
>>
>>> Many thanks. Is it possible that GROMOS parameters re also available in
>>> similar format like CHARMM? With GROMACS there is only  aminoacids.rtp
>>> provided for recent GROMOS parameters. In general, I see only protein,
>>> dna,
>>> rna and lipid parameters are provided in code (included in /top directory)
>>> but not for carbohydrates. Do I need to get GROMOS one from literature ?
>>>
>>>
>> They're included in aminoacids.rtp for every GROMOS force field, but those
>> parameters likely aren't the latest (since they go back to 43A1), so you'll
>> have to replace them or create your own force field directory with updated
>> parameters.  Check the user contributions page or the ATB server; they may
>> have the latest files.
>>
>> -Justin
>>
>>
>>
>>>
>>> On Fri, Mar 20, 2015 at 5:36 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>>>
>>>> On 3/20/15 12:30 PM, mish wrote:
>>>>
>>>>   Many thanks.  I know parameters are available in literature but my
>>>>> question
>>>>> was how to use them in GROMACS. Now, I can see different residue names
>>>>> (e.g  AMAN, BMAN, AGAL, BGAL etc for different monosaccharides in
>>>>> CHARMM).
>>>>> I think I will need to edit input pdb file accordingly. However, I am
>>>>> still
>>>>>
>>>>>
>>>> Yes, .rtp and coordinate file residue names must match.
>>>>
>>>>    not sure of methylated monosaccharides have to be constructed as
>>>> "modified
>>>>
>>>>> monosaccharides", or there are CHARMM parameters for methy (as  a
>>>>> separate
>>>>> residue) available and one should use 2 residues in such case. I will
>>>>> have
>>>>> a look in archive to find-out how to create  modified monosaccharides.
>>>>>
>>>>>
>>>>>   In CHARMM, there are "patches" that are applied to various residues.
>>>> There is limited support for such modifications in GROMACS.  You can
>>>> define
>>>> .tdb entries, but those only work for Protein, DNA, and RNA.  So you
>>>> should
>>>> not define separate residues for, e.g. a monosaccharide and a methyl
>>>> "residue."  Instead, a methylated sugar as a single .rtp entry is the
>>>> foolproof approach.  Chapter 5 of the manual is your friend (.rtp syntax
>>>> is
>>>> straightforward) as well as http://www.gromacs.org/
>>>> Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
>>>>
>>>> -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 | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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>> Gromacs Users mailing list
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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

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