AMBER Archive (2009)

Subject: Re: [AMBER] loading a following attached protein in amber 10

From: albert albert (albertassonke_at_googlemail.com)
Date: Tue Sep 08 2009 - 12:43:55 CDT

Many thanks for all,

warm regards

Albert

On Tue, Sep 8, 2009 at 7:27 PM, case <case_at_biomaps.rutgers.edu> wrote:

> On Tue, Sep 08, 2009, albert albert wrote:
> >
> > I don't know if you can help me to know why amber 10 cannot loading the
> > following attached file.
>
> It would helpful if you posted what you tried, and what the result was.
>
> Here's what I get:
>
> tleap -f leaprc.ff99SB
> > x = loadpdb pdb3brp.ent
>
> ....
>
> Unknown residue: MEN number: 229 type: Nonterminal
> Unknown residue: BLA number: 329 type: Terminal/last
>
> Amber's standard libraries only know about "ordinary" protein and nucleic
> acid
> residues, not about everything that could possibly be in a PDB file. See
> Tutorial B4 for an introduction to how to deal with non-standard residues.
>
> ...dac
>
>
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