dear justin Fatal error: [ file spc.itp, line 46 ]: Atom index (1) in settles out of bounds (1-0). This probably means that you have inserted topology section "settles" in a part belonging to a different molecule than you intended to. In that case move the "settles" section to the right molecule.
I checked topology file and sent topology and spc.itp file. please guide me. this is my topology file : ; Include forcefield parameters #include "ffamber03.itp" ; Include chain topologies #include "c_A.itp" #include "c_B.itp" ; Include water topology #include "spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include generic topology for ions #include "ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound #mols Protein_A 1 Protein_B 1 SOL 7127 this is my spc.itp file: [ moleculetype ] ; molname nrexcl SOL 2 [ atoms ] ; nr type resnr residue atom cgnr charge mass #ifdef _FF_GROMACS 1 OW 1 SOL OW 1 -0.82 2 HW 1 SOL HW1 1 0.41 3 HW 1 SOL HW2 1 0.41 #endif #ifdef _FF_GROMOS96 #ifdef HEAVY_H 1 OW 1 SOL OW 1 -0.82 9.95140 2 H 1 SOL HW1 1 0.41 4.03200 3 H 1 SOL HW2 1 0.41 4.03200 #else 1 OW 1 SOL OW 1 -0.82 15.99940 2 H 1 SOL HW1 1 0.41 1.00800 3 H 1 SOL HW2 1 0.41 1.00800 #endif #endif #ifdef _FF_OPLS 1 opls_116 1 SOL OW 1 -0.82 2 opls_117 1 SOL HW1 1 0.41 3 opls_117 1 SOL HW2 1 0.41 #endif #ifdef _FF_CHARMM 1 OW 1 SOL OW 1 -0.82 2 HW 1 SOL HW1 1 0.41 3 HW 1 SOL HW2 1 0.41 #endif #ifdef FLEXIBLE [ bonds ] ; i j funct length force.c. 1 2 1 0.1 345000 0.1 345000 1 3 1 0.1 345000 0.1 345000 [ angles ] ; i j k funct angle force.c. 2 1 3 1 109.47 383 109.47 383 #else [ settles ] ; OW funct doh dhh 1 1 0.1 0.16330 [ exclusions ] 1 2 3 2 1 3 3 1 2 #endif
_______________________________________________ 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/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/mailing_lists/users.php