<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><BR>Dear All Users<BR> <BR>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). <BR>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:<BR>"Fatal error:<BR>[ file tip3p,itp, Line 42 ]:<BR>Atom index (1) in settles out of bounds (1-0). ....."<BR>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. <BR>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. <BR>please guide me.<BR>thank you so much<BR>Best<BR> <BR>Sara Azhari<BR>Phd Student</td></tr></table><br>