Re: Brief courses on AMBER 6

From: Jarrod Smith <>
Date: Fri 01 Sep 2000 12:12:42 -0500

Jarrod Smith wrote:
> Below is a simple perl script that I use to take care of
> mapping MSI's flavor of amino acid PDB atom names to a LEaP/all_amino94
> compatible naming scheme.

A couple of people have contacted me indicating that they intend to use
the above mentioned script that I posted a couple days back. So I
thought I should point out that since then, a better tool for the job
has been shown to me by David Case. Namely, protonate. For example:

protonate -d $AMBERHOME/dat/PROTON_INFO < my.pdb > amber.pdb

will fix up the proton names as well as pro-chirality, the latter of
which my simple script cannot. Another nice feature is the -p flag,
which exhaustively reports the substitutions that protonate has made.

Sorry if this is obvious to some. I had mistakenly thought protonate
was specifically for adding protons to pdb derived from X-ray
structures. It seems that it can do much more.



Jarrod A. Smith
Research Asst. Professor, Biochemistry
Asst. Director, Center for Structural Biology
Computation and Molecular Graphics
Vanderbilt University
Received on Fri Sep 01 2000 - 10:12:42 PDT
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