AMBER Archive (2003)

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

From: bishop (bishop_at_tulane.edu)
Date: Fri Nov 07 2003 - 15:59:46 CST

let me knwo what folks say if they don't post to the amber site.

TOm

Endres, Robert G. wrote:

> 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
>>>
>>>
>>>
>>>
>>>
>>>
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>>>
>>
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>
>
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