Hi, I'm using the OPLS force field. [ PHE ] [ atoms ] N opls_238 -0.500 1 H opls_241 0.300 1 CA opls_224B 0.140 1 HA opls_140 0.060 1 CB opls_149 -0.005 2 HB1 opls_140 0.060 2 HB2 opls_140 0.060 2 CG opls_145 -0.115 2 CD1 opls_145 -0.115 3 HD1 opls_146 0.115 3 CD2 opls_145 -0.115 4 HD2 opls_146 0.115 4 CE1 opls_145 -0.115 5 HE1 opls_146 0.115 5 CE2 opls_145 -0.115 6 HE2 opls_146 0.115 6 CZ opls_145 -0.115 7 HZ opls_146 0.115 7 C opls_235 0.500 8 O opls_236 -0.500 8
I want to attach "CL" atom instead of HZ i made my pdb but when i use pdb2gmx, it adds HZ automatically in gro and top files. What should i do to get rid of this HZ and attach CL instead. (I edited top and gro files and remove HZ from them, it seemed to work properly at first, but when i tried to do energy minimization, it had errors in top file and i realized that it couldn't recognized the bond between CL and CZ): ERROR 1 [file topol.top, line 150]: No default Bond types ERROR 2 [file topol.top, line 422]: No default Angle types ERROR 3 [file topol.top, line 423]: No default Angle types *"topol.top":* ... 58 opls_146 3 PHE HE2 22 0.115 1.008 ; qtot 0.9 59 opls_145 3 PHE CZ 23 -0.115 12.011 ; qtot 0.785 60 opls_271 3 PHE C 24 0.7 12.011 ; qtot 1.6 61 opls_272 3 PHE O1 24 -0.8 15.9994 ; qtot 0.8 62 opls_272 3 PHE O2 24 -0.8 15.9994 ; qtot 0 63 opls_135 4 EtOH CB 25 -0.18 12.011 ; qtot -0.18 64 opls_140 4 EtOH HB1 25 0.06 1.008 ; qtot -0.12 65 opls_140 4 EtOH HB2 25 0.06 1.008 ; qtot -0.06 66 opls_401 5 CL CL 26 -1 35.453 ; qtot -1.06 ... [ bonds ] ... 59 66 1 60 61 1 60 62 1 63 64 1 63 65 1 ... [ angles ] ... 58 57 59 1 55 59 57 1 55 59 66 1 57 59 66 1 45 60 61 1 45 60 62 1 61 60 62 1 64 63 65 1 ...
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists