AMBER Archive (2004)

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

From: Peter Oelschlaeger (poe_at_caltech.edu)
Date: Fri Mar 05 2004 - 14:47:59 CST

David,

thanks for the help. Protonate now worked for me. In the long run, it
might be nice to increase the possible number of atoms (I think now it
is constrained to 7000).
For the conversion of the new pdb file to a bgf file, I used Open Babel,
a very handy program.

Best regards,

Peter

On Fri, 2004-03-05 at 08:16, David A. Case wrote:
> 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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