[gmx-users] Carbohydrate force fields in GROMACS

[Marcelo Depólo]

2015-03-20 14:21 GMT-03:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> 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.


You can find the forcefield here: http://dqfnet.ufpe.br/biomat/Software.html,
provided by one of leaders of the paper.


> 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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>>
>>
>>
> --
> ==================================================
>
> 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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-- 
Marcelo Depólo Polêto
Student of MSc Cell and Molecular Biology - UFRGS (Brazil)
B.Sc. Biochemistry - University of Viçosa (Brazil)