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
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Received on Fri Aug 04 2017 - 15:30:02 PDT
