Re: [AMBER] Units used in ff14sb

From: John Chodera <jchodera.gmail.com>
Date: Tue, 6 Feb 2018 18:18:47 -0500

Hi Sid,

The OpenMM XML forcefield file format is documented here:

http://docs.openmm.org/latest/userguide/application.html#creating-force-fields

All quantities should be in the OpenMM natural unit system:

http://docs.openmm.org/latest/userguide/theory.html#units

If you are trying to convert Amber parmameters or read them into a Python
program, I'd highly suggest you use the excellent ParmEd tool from Jason
Swails to read the original Amber files directly:

http://parmed.github.io/
https://github.com/ParmEd/ParmEd

We used ParmEd to convert the Amber files to OpenMM XML format, so using
the Amber files directly is likely to be much more reliable.

All the best

John

--
John D. Chodera
Assistant Faculty Member, Computational Biology
Memorial Sloan-Kettering Cancer Center
email: j <choderaj.mskcc.org>ohn.chodera.choderalab.org
office: 646.888.3400
fax: 510.280.3760
mobile: 415.867.7384
url: http://www.choderalab.org
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Received on Tue Feb 06 2018 - 15:30:02 PST