AMBER Archive (2009)

Subject: Re: [AMBER] loadpdb

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Tue Sep 08 2009 - 21:53:32 CDT

> ligand C
> ATOM 36 C52 RES d 1 -6.820 3.764 7.573 0.00 0.00 p1
> ligand C
> TER 37 RES d 1
> ATOM 1 C5' DG 1 4 -1.948 -4.520 9.025 1.00 0.17

(Note that the TER card means there is no covalent bond between
ligand & DNA.)

> When I try loadpdb
>
> > h3 = loadpdb xh3.pdb
> Loading PDB file: ./xh3.pdb
> Unknown residue: RES number: 0 type: Terminal/last
> ..relaxing end constraints to try for a dbase match
> -no luck
> Creating new UNIT for residue: RES sequence: 1
> Created a new atom named: C1 within residue: .R<RES 1>
> Created a new atom named: C2 within residue: .R<RES 1>
 ...

You should go over any examples on setting up new residue templates.

> Added missing heavy atom: .R<DG 2>.A<C5' 5>
> Added missing heavy atom: .R<DG 2>.A<P 1>
> Added missing heavy atom: .R<DG 2>.A<O1P 2>
> Added missing heavy atom: .R<DG 2>.A<O2P 3>

It looks like your initial DNA is not a terminal residue. If it's not
covalently linked to RES, it should probably be D5G or DG5 or some such.
('list' in leap should show all the defined residues.)

Bill

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