AMBER Archive (2006)

Subject: Re: AMBER: Backbone & Sidechain atoms: Definition

From: Zu Thur Yew (yewzt_at_intern.bii-sg.org)
Date: Thu Aug 24 2006 - 12:32:14 CDT

Hi,

Sorry for the lack of information..I was refering to MMPBSA decomp
results...trying to rationalise the results..

Thanks,

ZT

David A. Case wrote:
> On Thu, Aug 24, 2006, Zu Thur Yew wrote:
>
>> I read from the Amber mailing list that N, H, C, O, CA, and HA (and
>> HA2,3) are considered "backbone"....
>>
>> I know it sounds silly, but I would just like to confirm that H1,H2,H3
>> on the Nterm are considered "sidechain"?
>>
>
> Context is missing here. If some program is interpreting the terms "backbone"
> and "sidechain", then you need to say which program; maybe you can run some
> simple tests to find out what that program is doing (and/or look at the source
> code).
>
> If you are just using the term yourself, you can do whatever you want.
> I would classify H1,H2,H3 as backbone, but I've really never given it much
> thought.
>
> ...dac
>
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