AMBER Archive (2006)

Subject: Re: AMBER: Ring of dna

From: f m (floramactavish_at_hotmail.com)
Date: Tue Jul 18 2006 - 09:30:03 CDT

Thankyou, I think its working now. I minimised it and it created some
files.

Flora

>From: Bill Ross <ross_at_cgl.ucsf.edu>
>Reply-To: amber_at_scripps.edu
>To: amber_at_scripps.edu
>Subject: Re: AMBER: Ring of dna
>Date: Mon, 17 Jul 2006 12:15:10 -0700 (PDT)
>
> > I have deleated the addPdbResMap section of the leaprc.ff99 file. I
>think
> > that would stop it from converting the final residues to terminal
>residues.
> > I meant that my original pdb file had o3T atoms in the terminal
>residues. I
> > have just tried changing these to O3* but that made no difference. The
> > saveamberparm command won't work.
>
>Best to
>
> - make sure that your terminal residues are named as non-terminal in pdb
> - delete any atoms that don't belong in them
> - load pdb, let leap add any needed atoms
> - add circle-closing bond
> - saveamberparm
>
>O3* is not an amber ff atom name. Changing atom name alone doesn't
>fix the charge or atom type.
>
>Bill
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