You cannot find such a number because how will you define a
"base-stacking"? You better calculate the overlap areas of the bases with
respect to time using X3DNA. Overlap areas of the bases will tell you how
stacking is (strong or weak).
Ilyas Yildirim, Ph.D.
-----------------------------------------------------------
= Department of Chemistry - 2145 Sheridan Road =
= Northwestern University - Evanston, IL 60208 =
= Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
=
http://www.pas.rochester.edu/~yildirim/ =
-----------------------------------------------------------
On Thu, 8 Mar 2012, amir abbasi wrote:
>
> I meant number of base-stackings trough trajectory.
> In the other words how many base-stacking do I have?
>
>> From: amirhosseintaghavi786.hotmail.com
>> To: amber.ambermd.org
>> Date: Thu, 8 Mar 2012 17:18:27 +0000
>> Subject: Re: [AMBER] Base stacking
>>
>>
>> Hi,
>>
>> would you please be more precise..what do you mean by base stacking number??
>>
>>
>>
>>> From: amir-abbasi.hotmail.com
>>> To: amber.ambermd.org
>>> Date: Thu, 8 Mar 2012 14:43:51 +0330
>>> Subject: [AMBER] Base stacking
>>>
>>>
>>> Hi!
>>> I want to extract base stacking number from mdcrd file.
>>> Is there any analyzing program to do this or not?
>>> Best regards,
>>> Amir
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 08 2012 - 11:00:03 PST
