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.scripps.edu on behalf of Yong Duan
> Sent: Tue 10/14/2003 4:15 PM
> To: amber.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.scripps.edu
>>[mailto:owner-amber.scripps.edu] On Behalf Of Carlos Simmerling
>>Sent: Tuesday, October 14, 2003 3:19 PM
>>To: amber.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.ornl.gov>
>>To: <amber.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.scripps.edu
>>>To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>>>
>>>
>>>
>>
>>--------------------------------------------------------------
>>---------
>>The AMBER Mail Reflector
>>To post, send mail to amber.scripps.edu
>>To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>>
>>
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
>
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
--
http://dna.cbr.tulane.edu
Tulane University
Dept. of Environmental Health Sciences(SL-29)
School of Public Health & Trop. Medicine
1430 Tulane Avenue
New Orleans, LA 70112
Phone: 504-988-6203 Fax: 504-585-6428
Thomas.Bishop.tulane.edu
-----------------------------------------
-----------------------------------------
Xavier University
Division of Basic Pharmaceutical Sciences
College of Pharmacy
7325 Palmetto Street
New Orleans, LA 70125
Phone: 504-485-5106 Fax: 504-485-7930
tbishop.xula.edu
-----------------------------------------
-----------------------------------------
Center for Computational Sciences
Voice: (504) 862-8391/Fax: (504) 862-8392
-----------------------------------------
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Fri Nov 07 2003 - 22:53:01 PST
