http://upjv.q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#27 Provides an
example of developing a nucleic acid force field, and gives a brief
overview of how it was done in AMBER in regards to capping.
On Fri, Aug 4, 2017 at 3:29 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> ACE and NME are just for proteins, I believe. In the '94 FF,
> all_nucleic94.lib,
>
> > x = sequence { RG5 RG RG3 };
>
> > savepdb x.pdb
>
> gives you
>
> ATOM 1 H5T RG5 1 1.866 1.500 -0.000 1.00 0.00
> ATOM 2 O5' RG5 1 1.958 1.721 0.930 1.00 0.00
> ATOM 3 C5' RG5 1 0.788 2.111 1.674 1.00 0.00
> ATOM 4 H5'1 RG5 1 0.060 1.301 1.657 1.00 0.00
> ATOM 5 H5'2 RG5 1 0.351 3.002 1.223 1.00 0.00
> ...
>
> ATOM 98 O2' RG3 3 12.424 5.380 1.562 1.00 0.00
> ATOM 99 HO'2 RG3 3 12.714 5.231 0.659 1.00 0.00
> ATOM 100 O3' RG3 3 11.648 5.876 3.815 1.00 0.00
> ATOM 101 H3T RG3 3 12.494 6.329 3.795 1.00 0.00
>
> I'm not sure how relevant that is.
>
> Bill
>
>
> On 8/4/17 2:48 PM, giulia palermo wrote:
> > Dear all,
> >
> > I am parametrising an RNA base (i.e., guanine) which terminates with 5-OH
> > at the end of the RNA chain.
> >
> > Following this tutorial:
> >
> > http://ambermd.org/tutorials/advanced/tutorial1/
> >
> > one has to add ACE and NME as capping residues at the end of the
> > non-standard molecule.
> > My question is: having an RNA bases, which terminates with 5'-OH , how
> > shell I cap the 3' extremity?
> > Which residue shell I use as capping residue? And, in case the residue is
> > not ACE nor NME, which charges shell I assign during the RESP fitting
> > procedure?
> >
> > thank you very much
> >
> > Best
> > Giulia
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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>
--
Andrew Schaub
Graduate Program in Chemical & Structural Biology
Tsai Lab, http:///www.tsailabuci.com/ <http://www.tsailabuci.com/>
Luo Lab, http://rayl0.bio.uci.edu/html/
University of California, Irvine
Irvine, CA 92697-2280
949-824-8829 (lab)
949-877-9380 (cell)
aschaub.uci.edu <http://www.linkedin.com/pub/andrew-schaub/9a/907/382/>
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Received on Sat Aug 05 2017 - 01:00:03 PDT
