First, I am looking for 1->4 and 1->6 linkages. In the top_all36_carb.rtf file I found different linkages for beta-glucose, but non for alpha-glucose. I am trying to make a simple chain with 1->4 linkages like below:
alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose. Then, I might need to branch them with1->6 linkage. I tried Glycan Reader, but it still crashes. MH > >> Thanks Justin. >> I have tried the CHARMM-GUI but it crashed. I might need to modify the order >> of the atoms in my PDB file, which I have created using GLYCAM-Web GUI. I >> have downloaded the “toppar_c36_feb16” but I did not find a manual on how to >> apply them (any suggestions?), so it did not go far. > > What you need to do depends on linkages. There are patches (PRES in CHARMM > .rtf files) that tell you how each residue is manipulated in the case of a > patch; refer to the CHARMM documentation online for specifics. The file > you'll need is top_all36_carb.rtf. > > Otherwise, use the force field files as a template to rename your input > structure so CHARMM-GUI can process it. This is probably the much faster > route. > > -Justin > >> I'll play with these two, and I'll be back. >> MH >>> On May 18, 2017, at 5:08 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>> >>> >>> >>> On 5/18/17 4:57 PM, Mohammad Hassan Khatami wrote: >>>> Hi, >>>> >>>> I am trying to run simulations on alpha-D-glucose polymers. I have done >>>> these simulations using AMBER and I am wondering if it is possible to run >>>> them employing CHARMM36 in GROMACS, as well? >>>> It seams that CHARMM36 in GROMACS has only implemented monomers of >>>> alpha-D-glucose as ”AGLC”. Is there a way to introduce the whole polymer >>>> to the GROMACS? >>>> >>> >>> Sure, you can treat it like any polymer, but you'll have to create the >>> internal monomer residues yourself from the patches in the original CHARMM >>> force field files. >>> >>> Or try CHARMM-GUI; it should handle what you need and give you all the >>> necessary GROMACS inputs. >>> >>> -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 <mailto:jalem...@outerbanks.umaryland.edu> > | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > <http://mackerell.umaryland.edu/~jalemkul> > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > <http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List> before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > <http://www.gromacs.org/Support/Mailing_Lists> > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users> or send > a mail to gmx-users-requ...@gromacs.org > <mailto: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.
