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

From: Lee-Ping Wang <>
Date: Tue, 10 Jun 2014 11:50:40 -0700

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).

- Lee-Ping

-----Original Message-----
From: Jason Swails []
Sent: Tuesday, June 10, 2014 11:30 AM
Subject: Re: [AMBER] Side chain and backbone-specific parameters.

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 - 12:00:02 PDT
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