AMBER Archive (2003)

Subject: RE: AMBER: infinitely long DNA (to Yong Duan)

From: Endres, Robert G. (endresrg_at_ornl.gov)
Date: Fri Nov 07 2003 - 14:50:17 CST

Hi Yong Duan, and other AMBER users,

I recently asked about DNA and periodic BC and you made
some interesting suggestions (see below). As it seems right
now the periodic BC don't work w.r.t bond energies, only to
non-bonding energies, i.e. the two "long" bonds connecting the two ends of
each strand don't become "short" once the periodic BC are turned on.

My question is if you ever got it to work in practise? Many thanks in advance.

Best regards,
  Robert

-----Original Message-----
From: owner-amber_at_scripps.edu on behalf of Yong Duan
Sent: Tue 10/14/2003 4:15 PM
To: amber_at_scripps.edu
Cc:
Subject: RE: AMBER: infinitely long DNA & moil-view?

It's possible, but not straight forward and probably requires a bit
coding.

1) You have to know the periodicity of your DNA (how many bp per turn)
and choose the one that exactly matches complete turns (13 bp, as I
recall).
2) Construct it and manually modify the end residues and connect the
ends. You'd need to define your own residues, for instance. You will see
two long bonds. But do not worry, they should become short once the PBC
is taken into account (and if everything goes extremely well).
3) Modify the presure scaling code (in runmd.f) to allow fixing
Z-dimension.
4) Construct a box with the helical axis of the DNA is aligned to
Z-axis.
5) Equilibrate water with Z-axis fixed while holding DNA stationary
(with constraints). Remember to use very conservative pressure coupling
factor. Here, strictly speaking it makes no physical sense by scaling
just X-Y dimensions.
6) Pray (or visit the Buhda or a girl/boy friend).

Having said all these, I wonder if you have compelling justification to
go through this much trouble?

Yong
*************
> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Carlos Simmerling
> Sent: Tuesday, October 14, 2003 3:19 PM
> To: amber_at_scripps.edu
> Subject: Re: AMBER: infinitely long DNA & moil-view?
>
>
> 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
> >
> >
> >
> >
> >
> --------------------------------------------------------------
> ---------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >
> >
>
>
> --------------------------------------------------------------
> ---------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu