AMBER Archive (2008)

Subject: Re: AMBER: antechamber

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Thu Oct 16 2008 - 16:25:17 CDT

On Thu, Oct 16, 2008, Marcela Madrid wrote:
>
> I am trying to generate a new residue using antechamber. How do I
> specify which are the head and tail atoms? I am having trouble with
> this. I can generate a single residue, for ex. by terminating the chain
> with H, but not one that is joined to other residues. I believe the
> tutorials on-line use xleap for this. Is it possible to use antechamber?
> One tutorial says I will need the file mainchain.dat.
> If so, what are the omit_name atoms?

Is this the "one tutorial" you are refering to?

   http://ambermd.org/antechamber/pro4.html

If not, see if that helps. Generally (although I have not done this in a
while) the omit_name atoms are those that are in the stand-alone molecule you
are using, but which are not in the residue you wish to create.

...others can chime in here as well!....dac

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