AMBER Archive (2000)

Subject: Re: Brief courses on AMBER 6

From: Jarrod Smith (jsmith_at_chazin.structbio.vanderbilt.edu)
Date: Fri Sep 01 2000 - 12:12:42 CDT

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.

Thanks,

Jarrod 

-- 
Jarrod A. Smith
Research Asst. Professor, Biochemistry
Asst. Director, Center for Structural Biology
Computation and Molecular Graphics
Vanderbilt University

jsmith_at_structbio.vanderbilt.edu