[gmx-users] Carbohydrate force fields in GROMACS

[mish]

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 ?



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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