On 4/10/14, 2:51 AM, gsettanni wrote:
Hi Justin and Roland, we are interested in simulating a glycosilated protein. We already have a pdb file (and psf topology) with the charmm/namd format/nomenclature. We managed to have pdb2gmx read the carbohydrate residues by adding the relative entries in the residuetypes.dat, however we have not yet been able to add the covalent bonds necessary to reproduce the correct branched carbohydrate chains. Is there any solution for that? Roland seems to have one, although suboptimal. would it be possible to share it?
Using specbond.dat might help, but often these types of patches will require modification of atom types depending on the linkage, so there isn't any solution completely within pdb2gmx that will suffice, outside of building a residue from the original PRES entries in the CHARMM files, which is what it sounds like Roland's program does.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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.
