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
Received on Fri Sep 01 2000 - 10:12:42 PDT
