Dear FyD,
I will appreciate that if you send me the force field.
By the way, do you have any ideas of building the backbone of GNA? As far as I know, NAB could bulid the backbone of A-DNA and B-DNA, but how the GNA?
Thanks a lot!
Mu Xia
Email: caoyang9012.gmail.com
At 2012-12-07 01:37:16,FyD <fyd.q4md-forcefieldtools.org> wrote:
>Dear Mu Xia,
>
>We built a force field topology database for GNA; it was validated by MD...
>It will be available in R.E.DD.B. when we will have time.
>
>I can send you the entire FF next week if you are interested...
>
>regards, F.
>
>
>> Our recent research is the MD of a non-standard nucleic acid, named
>> Glycol Nucleic Acid (GNA). The glycol unit has just three carbon
>> atoms which differs from DNA or RNA. Moreover, the base pairs were
>> replaced by aromatic substitutes in our system to examine the
>> interactions.
>>
>> Here come the problems. Since the backbone and "base pair" are both
>> non-standard:
>>
>> 1. How could I build a double strand helix of GNA in xleap or some
>> other programs?
>>
>> 2. How could I define the force field of the non-standard residues?
>> Just like using Antechamber to build the force field of the ligand?
>
>
>
>_______________________________________________
>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 Dec 06 2012 - 17:30:02 PST
