On 4/4/14, 1:46 PM, Ahmet yıldırım wrote:
Dear Justin, These parameters are present in literature. I think these bonds/parameters are correctly generated. You said "The previous topology output suggests not, because ZN is not renamed to ZNW". I do not know what to do.
Probably because the distance you have set in specbond.dat is incorrect. I'll ask again - are the His-Zn bonds correctly generated? If not, that's your problem. If they are, we'll have to do more digging. You can avoid the whole Zn-renaming and charge issue if you do as I suggested before and create a residue that contains Zn(HOH), not just ZN and then a separate residue for the water bound to it. Treat it as its own entity.
I added the OZ-HZ bond in ffbonded.itp. Unfortunately I get the same errors: ERROR 1 [file protein_Ion_chain_A2.itp, line 33]: No default Bond types ERROR 2 [file protein_Ion_chain_A2.itp, line 34]: No default Bond types ffbonded.itp: Zn NA 1 0.20500 16744.0 ;modified Zn NB 1 0.20500 16744.0 ;modified Zn OZ 1 0.23000 16744.0 ;modified OZ HZ 1 0.09572 221682.2 ;modified
Are you making these corrections in the right place? Does your .top call your modified force field? Are you modifying files in $GMXLIB or in the working directory?
-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.
