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.