sara wrote:
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). ....."
You've placed your #include statement in the wrong location.
http://www.gromacs.org/Documentation/Errors#Atom_index_(1)_in_bonds_out_of_bounds
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.
Without seeing the contents of your topology, no one can comment on whether or
not this is appropriate.
I think because of use ffcnt_oplsaa.itp , it can't include tip3p.itp.
You can #include any series of legitimate .itp files. In your case, you
probably have something nested inside another [moleculetype].
-Justin
but when I add this forcefield to tip3p.itp by hand this error again comes.
please guide me.
thank you so much
Best
Sara Azhari
Phd Student
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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