Maybe just rename your custom thr.itp THR and in other places to something else to avoid conflict with default version?amber03.ff is in gromacs-version/share/top folder. There you can find aminoacids files with default amber03 THR.
On Saturday, October 28, 2017, 3:54:41 PM GMT+3, rose rahmani <rose.rhm...@gmail.com> wrote: Hello, this is topol.top ------- ; Include forcefield parameters #include "amber03.ff/forcefield.itp" [ moleculetype ] ; Name nrexcl ZnS 3 #include "ZnS.itp" #include "thr.itp" ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Include water topology #include "./amber03.ff/tip3p.itp" [ system ] ; Name LYSOZYME in water [ molecules ] ; Compound #mols ZnS 1 THR 1 SOL 561 ----- i get this error Fatal error: Atomtype P5 not found For more information and tips for troubleshooting, please check the GROMACS --------- thr.itp file [ moleculetype ] ; molname nrexcl THR 1 [ atoms ] ;id type resnr residu atom cgnr charge mass 1 P5 1 THR BB 1 0 72 2 Nda 1 THR SC1 2 0 0 3 D 1 THR SC2 3 +0.31 36 4 D 1 THR SC3 4 -0.31 36 [virtual_sites2] ; Site from funct a 2 3 4 1 0.5 [bonds] ; i j funct length force.c. 1 2 1 0.26 9000 [constraints] ; i j funct length 3 4 1 0.28 ------------------------------------ i think the problem is thr.itp file and its not usable for amber03 so what should i do?do you think the problem is that? i really appreciate you if you help me with regards rose -- 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.