Re: amber-developers: leaprc questions

From: David A. Case <>
Date: Mon, 2 Apr 2007 17:26:57 -0700

On Mon, Apr 02, 2007, Scott Brozell wrote:

> But if one sources leaprc.ff03 then one can load a dna containing pdb
> and save the prmtop.
> What is the equivalent procedure for a rna containing pdb ?

Leaprc files are templates that perform certain common tasks. I suppose we
could create various ways of doing protein-rna complexes, and encode them in
their own leaprc files. RNA-protein interactions may be an important special
case, but we can't "black-box" everything: basically, people need to learn how
to modify existing leaprc files to do what they want. This probably applies
to DOCK users as well....

But this is all going away with pdb version 3, where residue names for DNA
and RNA are disambiguated. Of course, people with old format pdb files will
have to convert them, but that seems more straightforward than to continue to
try to support all possible combinations. $.02.....dac
Received on Wed Apr 04 2007 - 06:07:33 PDT
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