On Wed, Jul 18, 2012, Rahul Banerjee wrote:
>
> I have started my refinement process from a structure derived from
> Cyana. Please check the atoms types input and the final output:
(Note: these are atom *names*, not atom *types*.)
> INPUT
> MODEL 1
> ATOM 1 N LYS A 1 1.329 0.000 0.000 1.00 13.00
> ATOM 2 H LYS A 1 1.806 0.000 0.856 1.00 5.14
> ATOM 3 CA LYS A 1 2.094 -0.002 -1.241 1.00 3.51
> ATOM 4 HA LYS A 1 1.783 0.852 -1.824 1.00 4.34
> ATOM 5 CB LYS A 1 3.590 0.118 -0.941 1.00 63.44
> ATOM 6 2HB LYS A 1 3.823 -0.496 -0.084 1.00 4.25
> ATOM 7 3HB LYS A 1 4.146 -0.245 -1.794 1.00 71.32
> FINAL OUTPUT after refinement
> MODEL 1
> ATOM 1 N LYS 1 53.840 52.435 33.926 0.00 0.00
> ATOM 2 H1 LYS 1 53.410 53.349 33.891 0.00 0.00
> ATOM 3 H2 LYS 1 54.818 52.392 33.680 0.00 0.00
> ATOM 4 H2 LYS 1 53.713 52.117 34.876 0.00 0.00
> ATOM 5 CA LYS 1 53.183 51.572 32.933 0.00 0.00
> ATOM 6 HA LYS 1 53.636 51.753 31.959 0.00 0.00
> ATOM 7 CB LYS 1 53.621 50.161 33.172 0.00 0.00
> ATOM 8 HB2 LYS 1 53.641 49.949 34.241 0.00 0.00
> ATOM 9 HB3 LYS 1 52.873 49.462 32.799 0.00 0.00
>
> I understand extra protons were added in the N-terminal by leap. But you
> can see the Beta-protons of LYS has different notations in different
> files. Similar differences are there all over all the other residues
> as well. Is it possible to convert the atom types same as Cyana-output
> after refinement?
It looks like cyana is still using an old atom nomenclature, whereas Amber
follows the current PDB format (version 3). When you say "after refinement",
do you mean after refinment in Amber, or in Cyana? It's not clear whether you
want to go from Cyana names to Amber names (tleap should do this
automatically) or from Amber names to Cyana.
[Aside: your "after" example above is rather odd, since the atom names are
in the wrong columns. How did you create that file?]
I'm actually not aware of any existing program that converts OUTPUT above to
INPUT above....why do you want to do that? That is, what would you do with
the files created by such a conversion? That said, hydrogen atom names have
been the source of many conversion pains...you might ask cyana users how they
convert PDB-format files.
...dac
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Received on Wed Jul 18 2012 - 10:00:03 PDT
