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

From: Jason Swails <>
Date: Tue, 10 Jun 2014 14:30:03 -0400

On Tue, 2014-06-10 at 10:50 -0700, Lee-Ping Wang wrote:
> Hi Jason,
> Thank you. I was mainly concerned that the frcmod format appears to support
> atom classes with a maximum of two letters (which would make hundreds of
> atom classes unwieldy), but your response sounds like this isn't a problem.
> I'm curious, how is this handled? Can I have multiple atom classes that use
> the same two letters (they just get used for different residues)?

Ah, that was your concern. You're correct -- this can be limiting.
Classes need to have unique names, although atom names are
case-sensitive and can take numbers as well as a number of ASCII symbols
(just be sure to avoid a . and :, as those are reserved for the atom
mask syntax). That should hopefully provide enough flexibility to
represent your whole parameter set...

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Jun 10 2014 - 11:30:03 PDT
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