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 <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. > -- 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.