I agree with David... XYZ is a very poor format, it hasn't information on atom names nor residues just elements and coordinates... you can ask packmol to directly output in PDB format (see keyword "filetype"), there is no need to further conversions...
Notice, this is true if your input molecule for packmol is a PDB, otherwise there is no way to fill the missing information...
Best,
Matias
------------------------------------
PhD.
Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay
[
http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
[
http://www.sirahff.com]
----- Mensaje original -----
De: "David Case" <david.case.rutgers.edu>
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Miércoles, 25 de Septiembre 2019 10:03:09
Asunto: Re: [AMBER] Packmol and Amber
On Tue, Sep 24, 2019, emanuele falbo wrote:
>
>I managed to create an file.xyz with multiple of my molecules by using
>packmol.
>Afterwards, I do convert the file.xyz into a file.mol2 and generate the
>topology and coordinates with tleap.
Convert to a pdb file instead of mol2, and see if that helps. Be sure
that there is a TER card between each molecule in the PDB file.
Amber support for multimolecule mol2 files may be broken: almost
everything we routine use this format for is for a single molecule.
...hope this helps...dac
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Received on Wed Sep 25 2019 - 07:30:02 PDT
