AMBER Archive (2006)

Subject: Re: AMBER: help creating RNA

From: sethl_at_gatech.edu
Date: Mon Jun 26 2006 - 10:42:00 CDT

Quoting "David A. Case" <case_at_scripps.edu>:

> On Thu, Jun 22, 2006, sethl_at_gatech.edu wrote:
> >
> > I have been fighting with leap in trying to build a simple RNA molecule.
> I've
> > been creating a DNA molecule and then modifying the .pdb file by changing
> the
> > residue names from "A" to "RA" for instance, but leap seems to complain
> quit a
> > bit. Can some one give me a quick protocol as to how to create an RNA
> molecule?
> >
>
> Just saying: "leap seems to complain quite a bit" is not very helpful. How
> about giving some details? Be sure to remove the H2'' atom from you pdb
> file,
> since this atom is not present in RNA. But without more information, one
> can really just guess about what might be going on.
>
> ....dac
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--

I do appologize for not being more specific.  I am attempting to model 2'5' RNA.
  I am attempting to do this by first creating a 3'5' structure, then loading in
my own custom residues.  I have modified some of the atom types and charges of
the residues (following a protocol that a collegue of mine documented a couple
of years ago).

According to his protocol, I would then need to change all of the Phosphate
bonds individually in Xleap and then the structure can be relaxed and built.  I
haven't gotten that far yet.  When I load the RNA structure into leap with the
new residues, leap does not make the connections among the atoms correctly.  The
resulting structure looks like a tangled spool of yarn and outputs the following
lines:

> rna = loadpdb eric25.pdb
Loading PDB file: ./eric25.pdb
  total atoms in file: 574
  Leap added 204 missing atoms according to residue templates:
       204 H / lone pairs

Additionally, there is no different behavior between loading the structure and
not loading in the custom residues and loading in the structure with the custom
residues.

Thanks for all of your help,

Seth Lilavivat
Georgia Institute of Technology

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