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.rosswalker.co.uk |
|
http://www.rosswalker.co.uk/ | PGP Key available on request |
> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of Guowen Han
> Sent: 10 August 2004 11:31
> To: amber.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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Received on Tue Aug 10 2004 - 19:53:01 PDT
