Dear Mu Xia,
> I will appreciate that if you send me the force field.
Yes; sorry I am late...
> 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?
You define the conformation for the GNA residues you wish in the FF
libraries. You construct the DNA analog of your GNA to the PDB file
format. You rename the residue names in the PDB file according to that
in the GNA FF lib. You remove the backbone in the PDB file; you load
all in LEaP, which will add the missing atoms; you run MD which should
lead you to a structure that makes sense.
regards, Francois
> 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?
>>
>>
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Received on Wed Dec 12 2012 - 22:00:03 PST
