AMBER Archive (2004)

Subject: Re: AMBER: conversion of Amber 7 .pdb file to .bgf file

From: David A. Case (
Date: Fri Mar 05 2004 - 10:16:19 CST

On Thu, Mar 04, 2004, Peter Oelschlaeger wrote:

> Then I get a pdb file with e.g. 2HB, 3HB instead of 1HB, 2HB.

Oops. Forgot about this. Amber uses the IUPAC defined hydrogen names
recommended by the NMR community:

%A J.L. Markley
%A A. Bax
%A Y. Arata
%A C.W. Hilbers
%A R. Kaptein
%A B.D. Sykes
%A P.E. Wright
%A K. Wuthrich
%T Recommendations for the presentation of NMR structures of proteins and
nucleic acids
%J J. Biomol. NMR
%V 12
%P 1-23
%D 1998

Note that this exception _is_ documented on the ambpdb page in the Users'

> -aatm only creates chunk...

Have you installed bugfix.14?

> Then I tried to convert the files using protonate with -b, as written in
> the manual, but in our Amber7 copy option -b doesn't exist.

You want to use the PROTON_INFO.brook file to convert 2HB,3HB to 1HB,2HB, etc.

...good luck....dac


================================================================== David A. Case | e-mail: Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to