AMBER Archive (2006)

Subject: Re: AMBER: Ring of dna

From: f m (floramactavish_at_hotmail.com)
Date: Mon Jul 17 2006 - 06:32:01 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.

>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: Sat, 15 Jul 2006 10:55:07 -0700 (PDT)
>
> > The O3T atoms only occur on the final residues of the DNA.
>
>That's because your residues were converted to terminal ones
>when you loaded the pdb, which you need to avoid by either
>disabling the residue name mapping or using loadpdbusingseq
>or whatever the cmd is.
>
>Bill
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