Hi Justin, I am asked to focus on learning how to change and update the CHARMM36 parameters, so I could implement the future changes and patches easier. (Thus, I am not focused in the Glycan Reader, at the moment.)
Thank you! I think I now have a better understanding of what should I do. For each part of my polymer,i.e. the initial, the middle and the final part, I have to modify the AGLC molecule to represent each of these parts, seperately. So, lets say to introduce the 1->4 linkage, I need to to apply 14ba patch from the top_all36_carb.rtf into the merged.rtp file of GROMACS CHARMM36. In this case, I need to create a new version of [ AGLC ] molecule (lets call it [ AGLC14 ]) in the merged.rtp, with the changes below from the the top_all36_carb.rtf, applied to it: ! equatorial-axial 1->4 linkage PRES 14ba 0.02 ! (i)1->4(i-1) equatorial at C1 and axial at C4 dele atom 1HO4 dele atom 2HO1 dele atom 2O1 ATOM 1C4 CC3161 0.09 ! ATOM 1O4 OC301 -0.36 ! ATOM 2C1 CC3162 0.29 ! BOND 1O4 2C1 I have to remove the HO4, HO1 and O1 lines and modify the values for the C4, O4 and C1 atoms. Then, I need to add the bond of [ bond ] … O4 +C1 Then, I need to apply the bonds and angles parameters in the the top_all36_carb.rtf (below), into the merged.vsd file of the GROMACS CHARMM36. ! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) IC 1C3 1C4 1O4 2C1 1.5071 110.40 -86.30 121.00 1.3902 ! psi IC 1C4 1O4 2C1 2O5 1.4560 121.00 -130.97 108.63 1.4470 ! phi IC 2O5 1O4 *2C1 2C2 1.4470 108.63 -122.09 110.89 1.5316 IC 2O5 1O4 *2C1 2H1 1.4470 108.63 121.92 111.32 1.0837 I have figured out how to implement R(IK), T(IKJ), T(JKL) and R(KL) values into the merged.vsd file, except for the PHI values. Where (and/or how) should I put it? Am I on the right track? Thanks again for your help. MH > On May 19, 2017, at 5:36 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 5/19/17 9:57 AM, Mohammad Hassan Khatami wrote: >> 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. >> > > Linkages are not specific to the sugar; most are totally generic. A few > comments suggest specific usage and may be corner cases, but your patches > will be among 14aa, 14ab, 14ba, 14bb. > >> >> Then, I might need to branch them with1->6 linkage. > > Also totally possible. > >> I tried Glycan Reader, but itstill crashes. >> > > Uploading a correctly named PDB file should work in Glycan Reader or the > Quick MD Simulator, but "still crashes" is not diagnostic of anything. > Specific help with CHARMM-GUI should be brought to their attention, though. > > -Justin > >> 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> >>> <mailto:jalem...@outerbanks.umaryland.edu >>> <mailto:jalem...@outerbanks.umaryland.edu>> | (410) 706-7441 >>> http://mackerell.umaryland.edu/~jalemkul >>> <http://mackerell.umaryland.edu/~jalemkul> >>> <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> >>> <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> >>> <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> >>> <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> >>> <mailto:gmx-users-requ...@gromacs.org >>> <mailto: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. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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