Dear Yanmei Song: I used gromacs version 3.3.1. I update ffG45a3.rtp to include my molecule. When I run pdb2gmx using my molecules with the command: "pdb2gmx -f min_C16.pdb -o C16.pdb -p topol.top -ff G45a3" I got the error message: " Opening library file ffG45a3.rtp Opening library file /user/localgromacs/share/gromacs/top/aminoacid.dat Reading min_C16.pdb... ', 81 atomsin in water Opening library file /user/localgromacs/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 1 residues with 81 atoms chain #res #atoms 1 ' ' 1 81 All occupancies are one Opening library file ffG45a3.atp Atomtype 49 Reading residue database... (ffG45a3) Opening library file ffG45a3.rtp Using default: not generating all posible dihedrals Using default:excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing impropers on same bond as a proper ------------------------------------------------------- >>>> Program pdb2gmx, VERSION 3.3.1 >>>> Source code file: resall.c, line: 331 >>>> >>>> Fatal error: >>>> in .rtp file at line: " The molecule I added in the ffG45a3.rtp is in attached file Thank you very much indeed. Angel
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