2015-03-20 14:21 GMT-03:00 Justin Lemkul <jalem...@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 <jalem...@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 <jalem...@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 >>>>> >>>>> jalem...@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-requ...@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 >>> >>> jalem...@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-requ...@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 > > jalem...@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-requ...@gromacs.org. -- Marcelo Depólo Polêto Student of MSc Cell and Molecular Biology - UFRGS (Brazil) B.Sc. Biochemistry - University of Viçosa (Brazil) -- 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-requ...@gromacs.org.