Hello Mu Xia.
There are a couple of ways of doing this and each require quite some work.
I am working with PNA which is similar to what you are trying to do, so a
basic guideline to do it would be:
1- Each individual "GNA nucleotide" has to be parametrized using
experimental data (X-ray/NMR) or using high level QM calculations
2- Using the optimized structure, you can use the R.E.D. server (or R.E.D.
tools) to generate charges compatible with the AMBER force field.
3- Use antechamber to translate your structures to the GAFF force field,
combine the generated charges with the GAFF atom types.
4- Generate an FRCMOD file with the FF modifications using parmchk
5- Using LEAP, generate a library file for your new GNA nucleotide using
your structure file (mol2) and the FRCMOD file.
6. With your library file you can then load a PDB that contains your GNA
nucleotide with other molecules (like DNA) and generate prmtop and coords
As I said, there are a lot of details to this guide and always double check
that the generated prmtop and coords behave accordingly to what is expected.
Hope this helps!
Have a good day,
Rodrigo.
On Thu, Dec 6, 2012 at 6:01 PM, Mu Xia <muxiachuixue.163.com> wrote:
> 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?
> >
> >
> >
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>
>
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Received on Fri Dec 07 2012 - 09:00:02 PST
