[gmx-users] CNT topology

Justin A. Lemkul jalemkul at vt.edu
Thu Feb 24 13:24:56 CET 2011

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.


> 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].


> 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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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