AMBER Archive (2008)

Subject: Re: AMBER: antechamber

From: Marcela Madrid (mmadrid_at_psc.edu)
Date: Tue Oct 21 2008 - 12:02:54 CDT

thanks! Marcela

David A. Case wrote:
> 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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