Re: amber-developers: leaprc questions

From: Scott Brozell <>
Date: Mon, 2 Apr 2007 19:06:51 -0700


On Mon, 2 Apr 2007, David A. Case wrote:

> 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....

This is a reasonable position, but rna is a special case.
We could make life easier for our users
by eliminating stumbling blocks like irrelevant inconsistencies
between leaprc files. For example, I tried to diff dna rna leaprc pairs
in anticipation of using the patch command to convert a dna leaprc
file into an rna one, but this was not as simple as it should have been.


> 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.
Received on Wed Apr 04 2007 - 06:07:33 PDT
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