Re: [AMBER] [q4md-fft] Modify RNA's sugar and adding partial charges

From: FyD <>
Date: Mon, 16 Mar 2015 08:15:03 +0100

Dear Jacob,

> In addition to that, I would like to mention that I have posted my question
> on amber mailing list. May be they can give me some alternative which I can
> do easily.

We have implemented the Amber approach developed by Cieplak et al. in PyRED...

> I am still strugling with my problem as I couldn't understand much from the
> tutorial you suggested me as I am very new to computational field. Hope I
> will get it soon:-)

To understand load an Amber force field in LEaP:

xleap -f leaprc.ff99SB (or whatever new version)
edit DC # to visualize the structure
edit DC3
edit DC5

> charge DC # to display the total charge
Total unperturbed charge: -1.000000
Total perturbed charge: -1.000000
> charge DC3
Total unperturbed charge: -0.692100
Total perturbed charge: -0.692100
> charge DC5
Total unperturbed charge: -0.307900
Total perturbed charge: -0.307900

-0.6921 + -0.3079 = -1.0000
charge (DC3 + DC5) = charge DC; idem for A, C, G, U

You can see that to construct an oligonucleotide you need for each
nucleoside three fragments: the 5'-terminal, the central and the
3'-terminal ones...

TTT = sequence { DC5 DC DC3 }
charge TTT

To construct these 3 fragments, you need to start from a nucleo_SIDE_
and dimethylphosphate:

and force the charges of some groups of atoms to take some values to
be compatible with Amber values; i.e. use inter-molecular charge
constraints during the charge fitting step; then PyRED does the job,
generate the FF libs, the FF parameters as well as a LEaP script...

Create a nucleoside for your modified nucleoside & try:

to try to not be lost by the files generated by PyRED ;-)

Run a PyRED job, then request for help if needed; see:
When describing the problem you encountered with R.E.D. Server
Development, please also provide the 'PXXXX' R.E.D. Server Development
job name in the body of your email so that we can more easily assist

I hope this helps...

regards, Francois

> On Mar 14, 2015 6:49 PM, "FyD" <> wrote:
>> Dear Jacob,
>> I have downloaded a RNA molecule pdb from Nucleic acid databse. When I am
>>> trying to modify its sugar ring ( as I want to cleave its c2' - c3' bond),
>>> loading it again in leap (AMBER) giving me the unmodified structure.
>>> Please
>>> suggest how can I modify all sugar ring present in the RNA and how to add
>>> partial charges to the modified residues for MD simulations.
>> You need to generate the different fragments:
>> See
>> PyRED will generate a leaprc.cmd file that can be adapted to be directly
>> used in LEaP.
>> "loading it again in leap (AMBER) giving me the unmodified structure"...
>> -> difficult to help without looking at the problem...
>> "as I want to cleave its c2' - c3' bond"
>> -> so you have a non-cyclic molecule.
>> in general you first load the FF libraries corresponding to the different
>> required molecular fragments and then you load the PDB file (often the
>> experimental data) of an oligonucleotide. To get a match between the FF
>> libs and the PDB file, the residue & name names available in the FF libs
>> have to match these in the PDB file...
>> if the residue/atom names in the PDB file correspond to these of the
>> natural residues, I am not surprised LEaP tries to match/reconstruct the
>> natural residues (in particular if atoms are missing in the PDB file).
>> regards, Francois

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Received on Mon Mar 16 2015 - 00:30:02 PDT
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