Re: [AMBER] LJ parameters

From: Luis Simon <>
Date: Wed, 10 Mar 2021 18:14:57 +0100

Hi Hector

Probably someone will correct me if I am wrong but in a mol2 file, apart from cartesian coordinates and atom symbols, you could only find charges and atom types. The lennard jones parameters (as well as the other force field parameters) are read from .dat or .frcmod files and assigned to the atoms in the .mol2 files according to the atom types. In other words, atoms sharing atom types also share the LJ parameters but not the charges, that can be specified separately in either mol2 or frcmod files.



> On 10 Mar 2021, at 17:59, LOZANO ORDOÑEZ, HECTOR <> wrote:
> Hi all,
> I would like to obtain de Lennard - Jones parameters of a molecule from a mol2 file but I have not been able to discover how to do it. Is it necessary to run a first optimization calculation or is ir possible to obtain the parameters from a .sdf or .pdb file? Could yoy give me a hint of what command sequences should I use?
> Thank you.
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Received on Wed Mar 10 2021 - 09:30:03 PST
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