AMBER Archive (2006)

Subject: Re: AMBER: Ring of dna

From: M. L. Dodson (bdodson_at_scms.utmb.edu)
Date: Mon Jul 17 2006 - 09:56:03 CDT

On Mon, Jul 17, 2006 at 11:32:01AM +0000, f m wrote:
> 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

Use the loadPdbUsingSeq command instead of loadPdb in LEaP.

Example:
loadPdbUsingSeq DNAfile.pdb {DA DC ... DT}

where ... DA DC ... DT is the sequence of the DNA 

-- 
M. L. Dodson
Personal:       mldodson-at-houston-dot-rr-dot-com
Work:           bdodson-at-scms-dot-utmb-dot-edu
Work: four_zero_nine-772-2178             FAX: four_zero_nine-747-8608
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