AMBER Archive (2009)

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

From: case (case_at_biomaps.rutgers.edu)
Date: Tue Sep 08 2009 - 12:27:47 CDT

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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