Re: AMBER: Ring of dna

From: Bill Ross <>
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.

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Received on Wed Jul 19 2006 - 06:07:07 PDT
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