AMBER Archive (2003)

Subject: Re: AMBER: infinitely long DNA & moil-view?

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Tue Oct 14 2003 - 14:18:30 CDT

1) I do not think it is currently possible to have a bonded
partner to an image residue, but I may be wrong. This
would prevent you from doing the longer DNA.

2) the moil-view page has been down for a little while
due to a server problem, we hope to have it back up soon.
In the meantine, contact me if you want the most recent
version (10.2).

Carlos

----- Original Message -----
From: "Endres, Robert G." <endresrg_at_ornl.gov>
To: <amber_at_scripps.edu>
Sent: Tuesday, October 14, 2003 2:57 PM
Subject: AMBER: infinitely long DNA & moil-view?

> Dear Amber users,
>
> I have two questions:
>
> 1) is it possible to do simulations of a truely periodic DNA molecule?
Looking
> at the DNA tutorial it seems that the DNA has a only a finite oligomer,
solvated in a periodic box.
>
> 2) I tried to obtain the latest version of Moil-view (9.1. ?), but could
> not access the proper web pages or links from AMBER home page.
>
> Any suggestions welcome!
>
> Robert
>
>
>
>
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