On Fri, Feb 11, 2005, Ilyas Yildirim wrote:
> ...
> ATOM 21 N3 G5 1 6.848 -2.225 0.940
> ATOM 22 C2 G5 1 6.597 -0.986 0.550
> ATOM 23 N1 G5 1 5.325 -0.513 0.260
> ATOM 24 H1 G5 1 5.202 0.438 -0.030
> ATOM 25 P G 2 6.882 -5.338 6.560
> ATOM 26 O1P G 2 7.505 -5.970 7.750
> ATOM 27 O2P G 2 5.404 -5.201 6.610
> ATOM 28 O3' G 2 9.461 -1.229 8.060
> ATOM 29 O5' G 2 7.538 -3.907 6.290
> ATOM 30 C1' G 2 8.527 -0.626 4.580
> ...
> -------------------------------------------------------------------
>
> When I open this .pdb file in xleap, and edit it, I see that it is not an
> RNA but a DNA. (Prob. because of the residue naming, when a ff is called
> in xleap, it will see it as a DNA residue)
Use an appropriate leaprc file, like leaprc.rna.ff99, for example. Or, you
could edit the pdb file itself to add the "R"s. The PDB format has long used
A,C,G for both ribo- and deoxy-ribo nucleic acids, and there is no simple way
to get around the problem.
A better program might look for an O2' atom and try to make a good guess.
Patches are welcome.
.....dac
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sat Feb 12 2005 - 01:53:01 PST
