AMBER Archive (2004)

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

From: David A. Case (case_at_scripps.edu)
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'
Manual.

> -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 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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            |    http://www.scripps.edu/case
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