AMBER Archive (2008)

Subject: Re: AMBER: 3fe-4s cluster parameter file generation

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Sep 17 2008 - 13:04:32 CDT

> >Please Help with a suggestion.
>
> Either you will have to read the prep manual and keep trying until you
> figure it out, starting with my suggestion, or you could build the
> residue template by drawing it in xleap. In this case once it is drawn
> you could select and then edit the atoms to set atom names, types, and
> charges. Then saveoff the residue and use loadoff to load it later.
> You can also use saveamberprep with your drawn residue to see what
> the correct form would be.

Also, once you are able to define the topology correctly, you will need to
find or derive the resulting bond, angle, and torsion terms.

Bill
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