Hey,
is there an easy/uncomplicated protocol to generate topological files and/or force field files from any xyz structure file, which can then be used with a force field molecular dynamics package?
When I tried to convert a polymer chain (as xyz) for the use with gromacs, I tried the route via pdb-files, where then the residues were missing. In the end, after choosing a force field, I end up with empty files.
I am aware, that unlike in quantum chemical packages, bonds and several parameters have to be set, which makes several FF-MD packages somehow complicated for beginners.
Is there anyone, who can recommend any package/protocol, that makes the conversion of xyz files (any structure (protein, polymer, small molecules) ) to any file format to be used with FF-MD applications straight-forward? Just like, giving coordinates, automatically determine topology, assign FF parameters and then ready-to-go?
Thanks and kind regards,
Conrad
All the methods I found so far include uploading the mol2 to some webservice (like swissparam) and and then get something, that can be handled with the gromacs converter.
Anything else, or any other FF-MD package that I could test, where small molecules can easily be converted and treated? Without using a webservice.
Thanks,
Conrad
You can use Open Babel to convert an XYZ file to a format compatible with your force field of choice (e.g., PDB or GRO) and then further modify or assign parameters as needed.
With Avogadro (https://avogadro.cc/), you can open an XYZ file, visualize the molecule, and then use the built-in file export options to save it in a format compatible with your force field (e.g., PDB or GRO). Additionally, Avogadro provides an intuitive interface for modifying the molecule's structure, assigning charges, and adjusting other parameters as needed.
Hi Susanta Roy ,
thanks for the answer. I have already tried openbabel for the conversation, but it did not work as expected for the polymer. But I did not test the gro file format via openbabel but pdb-file.
And I will the old avogadro a try again ...
Thanks and regards,
Conrad
I had a look into avogadro and openbabel.
While openbabel and avogadro converts xyz structure to gro files, no topology is preserved. And furthermore, no force field parameters can be assigned. At least neither with avogadro 1.2.0 nor with openabel 3.1.0. Is there a chance to add the information a posteriori?
Thanks and regards,
Conrad
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