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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