Thanks for your suggestion Daniel.
Sorry I forgot to mention that I need to make this selection when using
the zalign.py script from the APR tutorial.
When using :102.CA
The error I receive from the script is
" :102.CA"
So I think that while the script uses a similar Syntax to that from
Amber Mask it does not actually use Amber Mask.
My workaround so far was to rename the residues I want to select in the
input pdb file. E.g. LYS to LYX.
My input now looks like this:
python2 zalign.py -f pdb/input.pdb -a1 :ARX.HD2 -a2 :SEX.CB -a3 :SEX.HA
-a4 :LYX.HE3 -r 0 -i ../apr.in
Afterwards I reverse this in the resulting align_z.pdb output file.
On 02/01/2017 03:52 PM, Daniel Roe wrote:
> Hi,
>
> For more info on the Amber mask selection syntax see sections 29.2.2
> or 20.1.1 in the Amber 16 manual.
>
> On Wed, Feb 1, 2017 at 8:05 AM, Andreas Tosstorff
> <andreas.tosstorff.cup.uni-muenchen.de> wrote:
>> :LYS.CA
> This will select CA atoms in residues named LYS.
>
>> My question is how to select one specifc LYS (e.g. LYS102) in case there
>> are several in the protein.
>>
>> I tried :102.CA and :LYS102.CA but it did not work.
> The second mask is invalid. The first should work. You need to provide
> more details (error messages etc) for us to help you further. Note
> that Amber residue numbers are not necessarily the numbers used in a
> PDB. Amber residue numbers always start from 1 and are sequential, so
> if you have a 220 residue protein the residues are numbered 1 to 220.
>
> -Dan
>
>>
>> Any suggestions?
>>
>> --
>> M.Sc. Andreas Tosstorff
>> Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
>> Department Pharmazie
>> LMU München
>> Butenandtstr. 5-13 ( Haus B)
>> 81377 München
>> Germany
>> Tel.: +49 89 2180 77059
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
M.Sc. Andreas Tosstorff
Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
Department Pharmazie
LMU München
Butenandtstr. 5-13 ( Haus B)
81377 München
Germany
Tel.: +49 89 2180 77059
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Received on Wed Feb 01 2017 - 07:30:03 PST
