AMBER Archive (2005)

Subject: Re: AMBER: Question on makeing up of missing atoms

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Fri Dec 09 2005 - 06:57:06 CST

from a fixed template. you might want to use some
other program to add them (auch as one of the
rotamer libraries or SCWRL).

Benjamin Juhl wrote:

> Hi,
>
> lately i am loading pdb files with lea. In these pdb files, some side
> chains are missing (only the 4 backbone atoms are in the file). Leap
> is completeing the missing atoms, but i couldn't find any information
> in the manual in what way those atoms are added exactly. Is a
> energeticaly beneficial conformation chosen or are the atoms simply
> added from a fixed template?
>
> Benjamin
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