Dear Martina,
As a user of PyRED you should not need to convert mol2/mol3 files into
PDB files; all is already available in your job. The inputs are
provided to the PDB file format by the user, and the PyRED outputs
after geometry optimization (quantum mechanics) are provided to the:
- PDB file format (without atom connectivities); here the idea is to
let the user (or the program) choose, where to put atom connectivities
(different choices can be made in particular, when you have a metal
center in your molecule)
- mol2/mol3 file format (with atom connectivities, can be affect with
a specific keyword); here the idea is different: a force field library
is generated with charges, atom types, atom names, (polarizabilities
if needed) - to be loaded in the LEaP program using a leap script.
regards, Francois
Quoting Martina Devi <martinadevi2011.gmail.com>:
> Dear AmberUsers
>
> How do I convert mol2 to pdb?
>
> Regards
> Martina
F.-Y. Dupradeau
---
http://q4md-forcefieldtools.org/FyD/
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Received on Wed Jun 29 2016 - 23:30:02 PDT
