Dear Rodrigo,
I do not think that a frcmod file is needed for GNA; and parm99 atom
types do handle the GNA case; i.e. GAFF is not useful in this case.
we have a R.E.D. version that perform atom typing by now.
yes LEaP is reaquired to associate the different FF libs.
regards, Francois
> 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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Received on Wed Dec 12 2012 - 22:30:04 PST
