AMBER Archive (2007)

Subject: Re: AMBER: problems in adding ACE and NME group

From: backy (backy_at_ibms.sinica.edu.tw)
Date: Thu Jun 28 2007 - 01:13:02 CDT

> I feel I should repeat my earlier question: are you *sure* you need
> capping
> groups on a protein? One reason this is somewhat hard is because almost
> no
> one else ever feels the need to do it.
>
> ...dac

Hi, dac:
Sorry, I am a little confused about that. So do you mean that even for a
protein with residue index( ex: 100-500), the capping process is no need as
its energy was minimized? If so, for this kind of protein, what is the
"common" charge assigned to the protein terminal?
Thanks.

backy

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