AMBER Archive (2006)

Subject: Re: AMBER: how to create 2'-5' RNA

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Mon Jun 26 2006 - 17:52:10 CDT

Dear Seth,

> I am attempting to model some 2'-5' RNA molecules (using Amber 8). In leap I
> edited RC, RC5, RG, RG5, etc not to have HO'2 atoms but to have HO'3 atoms. I
> saved these prep files changed them by hand to have the correct charges and atom
> types for O3', O2', C3', C2', and HO'3.

It is not easy to create the residue libraries for this particular project
you are doing. So, u have to be careful. Let me write my ideas on this:

1. First thing to do is to get the RESP charges for these residues. You
need to follow the RESP protocol for that.

2. Create each residue, and define what the tail and head atoms are in
xleap while creating your own RNA library.

3. You need to define the missing parameters in xleap. For instance, what
is the atom type of O2'? Be sure that there is no missing parameters.

4. I dont think that you can use all of the AMBER force field parameters
for this project. For instance, the connections are not anymore 3'-5' but
2'-5'. The parameters around 2' and 5' need to be redefined.

5. After doing all these modifications, xleap will understand the
structure. In the .prep file u sent, there is only one residue defined
(RG). U need to re-define/create the residues A,G,C,U (and the X2 and X5
residues).

Good luck. Best, 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
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  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
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