Re: [AMBER] Side chain and backbone-specific parameters.

From: Jason Swails <>
Date: Tue, 10 Jun 2014 15:07:35 -0400

On Tue, 2014-06-10 at 11:50 -0700, Lee-Ping Wang wrote:
> Hi Jason,
> Thanks. :) I think there are enough symbols I can use that don't contain
> letters (to avoid clashes with existing types); hopefully that won't be
> confusing. (e.g. 15, ^&, ;), etc).

Well there is no problem conflicting with type names from "other" force
fields with which no compatibility is expected. For instance, there is
no need to have a separate set of atom class names for ff99SB and
ff14ipq, since both are protein force fields and are used to the
exclusion of the other.

There are admittedly some parts of the Amber code that depend on
quasi-discernible atom type names (like carbons containing c or C),
although those are slowly being weeded out and the only ones left are
legacy (at least that I can recall).

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Jun 10 2014 - 12:30:03 PDT
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