AMBER Archive (2006)

Subject: Re: AMBER: Ring of dna

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Mon Jul 17 2006 - 14:15:10 CDT

> 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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