Incorrect Atom ID in data file

Hello,

I am Daniel I am a student at Austin Community College I started working with lammps this summer and I have ran into some issues with the data file that vmd writes. I am trying to make a carbon nanotube and solvent using vmd but when I write the data file vmd list the atoms incorrectly so when I run it in lammps and then put it through vmd it shows the wrong atoms. I looked at data file and noticed that the atoms were being assigned the wrong Atom for the carbon in the carbon nanotube it was assigned hydrogen and the water assigned as Beryllium, Helium and Lithium. I have gone through old emails but I can't seem to find a solution of this problem. I went through and changed the atoms one by one and it took really long furthermore when I ran the file in lammps I got the following error

Invalid atom type in Atoms section of data file (atom_vec_full.cpp:932)

Is there any way of writing the data file in vmd using topo writelammpsdata with the correct atoms

240 atoms
283 bonds
0 angles
0 dihedrals
0 impropers
4 atom types
1 bond types
0 angle types
0 dihedral types
0 improper types

-4.724500 4.832500 xlo xhi
-4.619500 5.842500 ylo yhi
-11.108999 48.466002 zlo zhi

# Pair Coeffs

Hello,

I am Daniel I am a student at Austin Community College I started working with lammps this summer and I have ran into some issues with the data file that vmd writes. I am trying to make a carbon nanotube and solvent using vmd but when I write the data file vmd list the atoms incorrectly so when I run it in lammps and then put it through vmd it shows the wrong atoms. I looked at data file and noticed that the atoms were being assigned the wrong Atom for the carbon in the carbon nanotube it was assigned hydrogen and the water assigned as Beryllium, Helium and Lithium. I have gone through old emails but I can't seem to find a solution of this problem. I went through and changed the atoms one by one and it took really long furthermore when I ran the file in lammps I got the following error

Invalid atom type in Atoms section of data file (atom_vec_full.cpp:932)

this is most likely due to a typo you made when editing the file.

Is there any way of writing the data file in vmd using topo writelammpsdata with the correct atoms

a) this is really a VMD question and not a LAMMPS question, thus you
should ask on the VMD mailing list.
b) topo writelammpsdata writes out whatever information it currently
has, so the problem has to originate from what kind of atom types you
assign beforehand. please also make sure you have the latest version
of the topotools plugin and an up-to-date VMD version to ensure you
are not running into a bug that has already been solved.
c) data in VMD like type information, can be set via VMD scripting and
applied to whole groups of atoms in very sophisticated ways using the
VMD Tcl scripting interface and particularly the atomselect command.
please have a closer look at examples of how topotools is applied to
build topologies and study the script interface section in the VMD
user's guide.

please note that the data file format in LAMMPS is extremely flexible
and when writing scripts to work with it, one has to make choices as
to how much flexibility one allows. the more flexibility is allowed,
the more the tool is dependent on the user providing suitable input
information. the more a tools decides to guess, adapt, and change by
itself, the less flexibility you have. the goal of topotools is to
provide a very flexible interface to experienced people. more
sophisticated and less flexible tools can be built on top of it (e.g.
the nanotube builder uses topotools underneath to generating topology
information).

axel.