[gmx-users] Carbohydrate force fields in GROMACS

[mish]

Many thanks :). It should be enough to start.

Best,
Mish


On Fri, Mar 20, 2015 at 6:32 PM, Thomas Piggot <t.piggot at soton.ac.uk> wrote:

> Hi,
>
> You can download the parameters from:
>
> http://dqfnet.ufpe.br/biomat/Software_files/GROMOS-53A6glyc.tar
>
> I have used them and they seem to perform fine. They are not too different
> from the previous 45A4/53A6 parameters.
>
> Cheers
>
> Tom
>
>
> On 20/03/15 17:21, Justin Lemkul wrote:
>
>>
>>
>> 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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>>>
>>>
>>>
>>
> --
> Dr Thomas Piggot
> University of Southampton, UK.
>
>
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