Dear David,
I have started my refinement process from a structure derived from Cyana. Please check the atoms types input and the final output:
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?
With best regards,
Rahul
________________________________________
From: case [case.biomaps.rutgers.edu]
Sent: Tuesday, July 17, 2012 8:38 PM
To: AMBER Mailing List
Subject: Re: [AMBER] How to convert AMBER atom type to CYANA
On Tue, Jul 17, 2012, Rahul Banerjee wrote:
>
> I was refining a NMR structureconsisting of 20 models derived from
> Cyana. After refining each model at the final step I have converted all
> the refined strucrures into corresponding PDBs. At this stage how can I
> convert Amber atom types to that of Cyana?
It's not clear what you mean, since PDB files don't contain atom types. Maybe
you could explain what you want to do next (i.e. after "converting Amber atom
types to Cyana).
....dac
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Received on Wed Jul 18 2012 - 07:30:02 PDT
