[gmx-users] Carbohydrate force fields in GROMACS

[Marcelo Depólo]

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.


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
>>>
>>> ==================================================
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/
>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>>>
> --
> ==================================================
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



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