As I repeatedly encountered difficulties with my metal-bound protein coordinates and checked for information in this mailing list I realized that I am not the only one in this case.
What I do:
- I use aria2.3 for my final structure calculation
- the metal site is defined (residues and atoms involved, bonds and angles) using cns to generate pdb and psf files (I posted example files on the aria mailing list) - as the ion is linked to the protein, torsion angle molecular dynamics is working fine (compare item 008576). These pdb and psf files as well as modified parameter and topology files are used throughout the aria calculation
- aria setup is done from the ccpnmr project containing resonance information and the noesy spectra with associated peak lists etc. This ccpnmr project is then modified during the calculation and will include relevant information (aria assigned peak lists, violation analysis and molecular coordinates) for structure analysis but also coordinate deposition (using ECI)
- aria is started using the aria2 run.xml command (not from within ccpnmr) and the final structural ensemble is found in the it8 or refine directory (it includes the metal ion).
- the coordinates generated during the aria calculation in the ccpnmr project DO NOT include the metal ion. I would have liked to understand how to do this, but did not succeed
Once I am ready for pdb submission, I create and complete an ECI Entry as described.
ATTENTION: NO special characters in here (°C, ä,ö etc) - if you do have, the first step of Entry submission via AutoDep does not work (error message: Login failed
There was a problem with the values that were entered. Either the file could not be located or the password that you entered was not valid. Please try again. )
Within the AutoDep interface I finish completion of the different entries - however, as mentioned above, the coordinate set from within the ccpnmr project does not include the metal ion. Therefore, I downloaded my refine/analysis concatenated pdb file from the aria directory, was asked whether I wanted to overwrite the existing coordinate file (important: do not delete it before downloading the new file) and just recorrected the HET section as requested.
Hope that helps
Beate
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