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 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.
Many thanks, Mish On Fri, Mar 20, 2015 at 5:00 PM, Marcelo Depólo <marcelodep...@gmail.com> wrote: > There is also a Modified GROMOS forcefield for glycans here: > > http://dx.doi.org/10.1021/ct300479h > > Cheers! > -- > 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. > -- 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.