Hi I think you should use the correct atomtype, accoding to this FF atomtypes, for your atom which you have introduced as HH.
Best Mohsen On Tue, Nov 19, 2013 at 7:48 PM, fatemeh ramezani <fr_...@yahoo.com> wrote: > HI DEAR USERS > I want to simulate collagen by OPLSAA. I added hydroxyprolin parameters as > follow: > > in .hdb file : > > HYP 5 > 1 5 HA CA N C CB > 2 6 HB CB CG CA > 1 6 HG CG CD CB > 1 6 HD CD N CG > 1 4 HH OH CG CD > > > in aminoacids.c.tdb file: > [ HYP-COO- ] > [ replace ] > CA CA opls_285 12.011 -0.09 > C C opls_271 12.011 0.7 > O O1 opls_272 15.9994 -0.8 > OXT O2 opls_272 15.9994 -0.8 > [ add ] > 2 8 O C CA N > opls_272 15.9994 -0.8 > [ impropers ] > CA O1 C O2 improper_O_C_X_Y > > [ HYP-ZWITTERION_COO- ] > [ replace ] > CA CA opls_246 12.011 0.13 > C C opls_271 12.011 0.7 > O O1 opls_272 15.9994 -0.8 > OXT O2 opls_272 15.9994 -0.8 > [ add ] > 2 8 O C CA N > opls_272 15.9994 -0.8 > [ impropers ] > CA O1 C O2 improper_O_C_X_Y > > > > in aminoacids.n.tdb file: > > [ HYP-COO- ] > [ replace ] > CA CA opls_285 12.011 -0.09 > C C opls_271 12.011 0.7 > O O1 opls_272 15.9994 -0.8 > OXT O2 opls_272 15.9994 -0.8 > [ add ] > 2 8 O C CA N > opls_272 15.9994 -0.8 > [ impropers ] > CA O1 C O2 improper_O_C_X_Y > > [ HYP-ZWITTERION_COO- ] > [ replace ] > CA CA opls_246 12.011 0.13 > C C opls_271 12.011 0.7 > O O1 opls_272 15.9994 -0.8 > OXT O2 opls_272 15.9994 -0.8 > [ add ] > 2 8 O C CA N > opls_272 15.9994 -0.8 > [ impropers ] > CA O1 C O2 improper_O_C_X_Y > > > in aminoacids.rtp file: > [HYP] > [ atoms ] > N opls_239 -0.140 1 > CA opls_246 0.010 1 > HA opls_140 0.060 1 > CB opls_136 -0.120 2 > HB1 opls_140 0.060 2 > HB2 opls_140 0.060 2 > CG opls_136 -0.120 3 > HG1 opls_140 0.060 3 > OH opls_167 -0.683 3 > HH opls_168 0.435 3 > CD opls_245 -0.050 4 > HD1 opls_140 0.060 4 > HD2 opls_140 0.060 4 > C opls_235 0.500 5 > O opls_236 -0.500 5 > [ bonds ] > N CA > CA HA > CA CB > CA C > CB HB1 > CB HB2 > CB CG > CG HG1 > CG OH > OH HH > CG CD > CD HD1 > CD HD2 > CD N > C O > -C N > [ impropers ] > -C CA N CD improper_Z_N_X_Y > CA +N C O improper_O_C_X_Y > > in ffbonded.itp file: > [ angletypes ] > ; i j k func th0 cth > CG CB OH 2 109.5 520.0 > OH CG CD 2 109.5 520.0 > CG OH HH 2 109.5 450.0 > > [ dihedraltype ] > CG CB CD OH 1 35.3 334.8 > > CB CG OH HH 1 0.0 1.3 3 > > > [ bondtype ] > CG OH 2 0.144 6100000.0 ; > > OH HH 2 0.100 15700000.0 ; > > > When I grompp, I get this error: > Unknown bond_atomtype HH > What does this error mean ? > > > Fatemeh Ramezani > -- > 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.