Geometry input file

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1

Dear All users

I built my model (a composite HAP + CNT) using material studio 6. The outputs of that program are like, file.pdb file.cif file.mol2 etc. In output file it is just atoms coordination and bonds between two atoms but I need to angle between three atoms. Here is my data file that I edited to Lammps input data file. What is direct way to make an appropriate input data file for Lammps? I waste so much time to converting manually .

Regards

materialstudiooutput.txt (112 KB)

lammpsdatafile.xyz (102 KB)

2

Dear All users

I built my model (a composite HAP + CNT) using material studio 6. The
outputs of that program are like, file.pdb file.cif file.mol2 etc. In output
file it is just atoms coordination and bonds between two atoms but I need to
angle between three atoms. Here is my data file that I edited to Lammps
input data file. What is direct way to make an appropriate input data file
for Lammps? I waste so much time to converting manually .

of course you can automate the process with some scripting
or writing a custom program to do the task. computers are
generally good at doing tedious tasks consistently (which humans
are usually bad at).

however, there is no simple way to convert some set of coordinates
automatically into into a perfectly working input deck for lammps.
this *cannot* work in general, since a lot of information is missing
and a program can only use the information your present, it does
not know what you mean by it or what it is supposed to represent.
so the script/program you write has to follow some conventions
that make it easy to reconstruct the missing information through,
e.g. naming conventions or conventions how to assign bond and
angles/dihedrals/impropers from the bonds and assign types to
them and match them with a database of force field data.

this procedure is well established for biomolecules like peptides,
since there is are established conventions in the protein database
and its corresponding file formats and the the fact that those
molecules are build from simple chains of a small number of
possible monomers (amino acids). as soon as you deviate from
that, things get complicated and require manual intervention.

to some degree you can find help in "meta tools" like andrew's
moltemplate or the topotools plugin for VMD, but the gruntwork
of how to define the conventions and how to map the atom names
and bond topology with force field parameters, is still left to you.

there ain't no escape from the blues. :wink:

axel.

3

Dear Ali

If you have built a system using the tools which come with materials
studio, for example (including bonds, atom charges, force-field
parameters). You could try using the "msi2lmp" tool to convert your
materials studio files to LAMMPS "DATA file" format. See:

(The msi2lmp tool was written in 2004, although I am under the
impression people still use it. Hopefully it works for you.)

Once you have created a LAMMPS DATA file, you can use
"gen_all_angles_topo.sh", "ltemplify/moltemplate" or "VMD/topotools"
to add angles, dihedrals, and impropers to your system.

1) Take a look at the "gen_all_angles_topo.sh" script.
http://www.moltemplate.org/other/index.html

2) Alternately, you can try using "ltemplify.py" script which comes
with moltemplate to convert it into moltemplate (.LT) format. If you
have molecules in addition to carbon, then you can create different LT
files for each molecule type. To generate angular interactions, you
can add "Data Angles By Type" sections to your LT file. See the many
instructions and examples in chapter 6 and appendix A of the
moltemplate manual. There is also an example of this online:

http://www.moltemplate.org/examples/translocation/monomer.lt
http://www.moltemplate.org/examples/translocation/polymer.lt

3) Alternatley, you can also use topotools. See:
https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---part-1

However, you still must manually assign coeffs for these interactions
(for example, using "pair_coeff", "bond_coeff", "angle_coeff",
"dihedral_coeff", and "improper_coeff" input script commands).

I hope this addresses your question.

   ---- automagic molecule builders ----

Ideally it sounds like many lammps users want a program which can read
a coordinate file (PDB or XYZ), generate bonds by distance, and angle
topology, and "automagically" determine the force-field parameters for
your system using a "canned" force field. There are commercial
programs which can do this. However I agree with Axel: I would not
automatically trust any such program without investigating it first.
There is no way to make this process completely automatic. At a
minimum, you would have to find out which type of canned force-field
works well with the type of molecules you are interested in studying.
(And, as Axel said, you have to be very careful with atom-type-names.)

  Although I have not used them, I am under the impression that
several commercial programs including AMBER and Materials Studio do
come with tools which can read a PDB files and XYZ files and assign
"canned" force-field parameters. AMBER comes with the GAFF force
field for general organic molecules. Materials Studio supports
several force-fields (http://msc.psu.edu/software/materials-studio).

  It would be nice if it was not necessary to use external commercial
programs like these. Unfortunately, neither topotools nor moltemplate
can do all of these steps, yet. (topotools does not yet assign
"coeffs", and moltemplate does not yet generate bonds-by-distance. As
mentioned earlier, both of these programs can generate angles,
dihedrals, and impropers, but you must manually assign coeffs for
these interactions yourself.)

  If someone has a favorite "canned" force-field style (such as GAFF,
DREIDING, COMPASS, CVFF, PCFF, UNIVERSAL), then I can offer lots of
advice if someone else if they are do the hard work of converting the
parameter settings into "moltemplate" (.LT) format. I do not use any
of these force-fields settings in my own work and do not understand
their file format. Someone else would have to volunteer their time
and expertise to make this happen, but I can help. (It's possible I
could also add some features to moltemplate to make this easier, such
having moltemplate automatically generate bonds-by-distance.)

  I hope this helps.
  Sorry this was such a long email rant.
  Good luck.

Andrew

"meta-tools like moltemplate and topotools"

Awesome. That's cool. ..I'm going to start calling it a meta-tool!