> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
Hi!,
You could use the attached awk script to make what you are looking for,
but … a couple of think first:
1. Your model has the NH3 terminus with H1, H2 and H2 hydrogens (two H2
hydrogens). I saw the same behaviour in some of my calculations, so I
think a FF error or a tleap or ambpdb error.
2. you could user the following command “gawk -f pdb2pdb.awk -v cyana=1
file.pdb” but …, it will change your NH3 terminus to 1H, 2H and, let say
3H.
3. Or, you could use the command “gawk -f pdb2pdb.awk -v preloc=2
input.pdb” to change "HXXn " to "nHXX".
You must to play around, best that nothing I hope this help you.
Greeting, Hector.
---------------------------------
Dr. Hector A. Baldoni
Area de Quimica General e Inorganica
Universidad Nacional de San Luis
Chacabuco 917 (D5700BWS)
San Luis - Argentina
hbaldoni at unsl dot edu dot ar
Tel.:+54-(0)266-4423789 ext. 157
----------------------------------
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jul 19 2012 - 08:00:02 PDT
