[gmx-users] CNT topology

sara sara_15_s at yahoo.com
Thu Feb 24 13:19:20 CET 2011

Dear All Users
I am beginner to GROMACS. I want to simulate CNT in water. I made pdb file by VMD and then made .gro by "editconf -f file.pdb -o file.gro -box 4" command. then for made topology file, I use .n2t itp, .itp, .rtp, ff.dat, and by "x2top -f file.gro -o topol.top -ff cnt_oplsaa -name CNT -noparam -pbc" command. it makes topology file. but when I want to add water by "genbox" it make "topology.top" but there is not the water parameters(there is only number of water molecules at the end of file). 
then I use #include command for tip3p.itp model. when I want do em run by grompp, it dos not make .tpr and give error:
"Fatal error:
[ file tip3p,itp, Line 42 ]:
Atom index (1) in settles out of bounds (1-0).   ....."
I studied some guides to another gromacs user in mailing list and add "#define ff.." in ffcnt_oplsaa.itp but it gives this error again. 
I think because of  use ffcnt_oplsaa.itp , it can't include tip3p.itp. but when I add this forcefield to tip3p.itp by hand this error again comes. 
please guide me.
thank you so much
Sara Azhari
Phd Student

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