Update to my earlier message:
On Thu, Jan 26, 2017, David Case wrote:
> On Thu, Jan 26, 2017, Paul Meister wrote:
>
> > Sorry for not being specific. The tRNA isn't bound through the phosphate
> > group, but is instead held to the protein through many hydrogen bonds. The
> > 5' terminal phosphate is supposed to participate in the reaction. The PDB
> > ID for this protein is 2DXI. Running the files through LEaP, it tells me
> > that there are no parameters for OP3, a phosphate oxygen. The mol2 file
> > from RED shows me that it is there and bound. I'm just not sure why there
> > are parameters for the other two oxygen atoms, but not for OP3.
>
> Try this: At the beginning of the tRNA, your PDB file looks like this:
>
> ATOM 1 OP3 G C 501 19.050 87.190 73.029 1.00 73.49 O
> ATOM 2 P G C 501 18.499 87.676 71.706 1.00 75.79 P
> ATOM 3 OP1 G C 501 16.984 87.888 71.715 1.00 73.44 O
> ATOM 4 OP2 G C 501 18.979 86.828 70.515 1.00 77.51 O
> ATOM 5 O5' G C 501 19.153 89.150 71.502 1.00 63.81 O
> ATOM 6 C5' G C 501 18.729 90.260 72.301 1.00 48.63 C
>
> Change this to this:
>
> ATOM 1 OP3 OHE C 500 19.050 87.190 73.029 1.00 73.49 O
> ATOM 2 P G C 501 18.499 87.676 71.706 1.00 75.79 P
> ATOM 3 OP1 G C 501 16.984 87.888 71.715 1.00 73.44 O
> ATOM 4 OP2 G C 501 18.979 86.828 70.515 1.00 77.51 O
> ATOM 5 O5' G C 501 19.153 89.150 71.502 1.00 63.81 O
> ATOM 6 C5' G C 501 18.729 90.260 72.301 1.00 48.63 C
>
** Important: you need to have update.21 for AmberTools16 applied: use
update_amber or configure in $AMBERHOME to achieve this.
** Also note: this is the way we have always handled 5' phosphates, but it
is not necessarily optimal. It yields a protonated phosphate group (net
charge of -1), and the charges on the phosphate group are the same as those
for the phosphodiester linkages within a nucleic acid chain. If these
approximations seem too severe, you will learn how to properly use the special
RED units (or build your own).
>
> ...dac
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 27 2017 - 07:00:02 PST
