AMBER Archive (2004)

Subject: RE: AMBER: unknown residue: ABA

From: Lao_3 (hgw2000_at_yahoo.com)
Date: Wed Aug 11 2004 - 10:45:44 CDT

The tutorial does not really help. It does not tell
how to create the .in files.

For my case, I only have the following data available,

HETATM 718 N ABA 95 55.470 50.317 -6.728
 1.00 7.56 3HVP 839
HETATM 719 CA ABA 95 54.746 50.747 -5.560
 1.00 6.09 3HVP 840
HETATM 720 C ABA 95 55.483 50.063 -4.381
 1.00 6.45 3HVP 841
HETATM 721 O ABA 95 56.102 48.982 -4.637
 1.00 6.91 3HVP 842
HETATM 722 CB ABA 95 53.282 50.363 -5.566
 1.00 2.25 3HVP 843
HETATM 723 CG ABA 95 52.355 51.547 -5.700
 1.00 2.00 3HVP 844

Could someone tell how should I start?

Thanks.

Guowen

--- Ross Walker <ross_at_rosswalker.co.uk> wrote:

> Dear Lao,
>
> I suggest you go through the amber tutorials on
> http://amber.scripps.edu/tutorial/index.html
>
> These will go over how the force field works and the
> issues involved with a
> classical approach. You should pay particular
> attention to the Plastocyanin
> tutorial
>
http://amber.scripps.edu/tutorial/plastocyanin/pcy-tutorial.html
>
> This covers how to deal with a non standard resiude,
> how to create and add
> parameters etc.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel:- +1 858 784 8889 | EMail:-
> ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk/ | PGP Key available
> on request |
>
>
> > -----Original Message-----
> > From: owner-amber_at_scripps.edu
> > [mailto:owner-amber_at_scripps.edu] On Behalf Of
> Guowen Han
> > Sent: 10 August 2004 11:31
> > To: amber_at_scripps.edu
> > Subject: AMBER: unknown residue: ABA
> >
> > I have error messages as follow:
> >
> > > mol=loadpdb 3hvp.pdb
> > Loading PDB file: ./3hvp.pdb
> > Unknown residue: ABA number: 66 type:
> Nonterminal
> > Unknown residue: ABA number: 94 type:
> Nonterminal
> > Creating new UNIT for residue: ABA sequence: 67
> > One sided connection. Residue: missing connect0
> atom.
> > Created a new atom named: N within residue: .R<ABA
> 67>
> > Created a new atom named: CA within residue:
> .R<ABA
> > 67>
> > Created a new atom named: C within residue: .R<ABA
> 67>
> > Created a new atom named: O within residue: .R<ABA
> 67>
> > Created a new atom named: CB within residue:
> .R<ABA
> > 67>
> > Created a new atom named: CG within residue:
> .R<ABA
> > 67>
> > One sided connection. Residue: missing connect1
> atom.
> > Creating new UNIT for residue: ABA sequence: 95
> > One sided connection. Residue: missing connect0
> atom.
> > Created a new atom named: N within residue: .R<ABA
> 95>
> > Created a new atom named: CA within residue:
> .R<ABA
> > 95>
> > Created a new atom named: C within residue: .R<ABA
> 95>
> > Created a new atom named: O within residue: .R<ABA
> 95>
> > Created a new atom named: CB within residue:
> .R<ABA
> > 95>
> > Created a new atom named: CG within residue:
> .R<ABA
> > 95>
> > One sided connection. Residue: missing connect1
> atom.
> > total atoms in file: 758
> > Leap added 791 missing atoms according to
> residue
> > templates:
> > 791 H / lone pairs
> > The file contained 12 atoms not in residue
> templates
> >
> > Please help!
> >
> > Lao_3
> >
> > __________________________________________________
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