AMBER Archive (2002)

Subject: Re: procheck

From: David A. Case (case_at_scripps.edu)
Date: Tue Nov 05 2002 - 10:31:31 CST

On Tue, Nov 05, 2002, hung_at_atc.atccu.chula.ac.th wrote:
>
> Does anybody experience "unrecognized atom type [CB ] in residue
> VAL 146" in PROCHECK? "CB" of all residues (154) were said to be
> unrecognized.
>

How are you making your pdb file? Be sure to use the "brookhaven"
formatting for atom names if you use ambpdb. This is the default in
Amber 7, but required a switch (I think is is "-brook") in earlier
versions. In any event, check the formatting of the CB cards in your
file against a genuine PDB file to see if you can spot formatting differences.

...dac 

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