Cyana Structures refinement
This example describes the Restrained Energies Minimization on a pre calculated solution structure from Xplor-NIH, Cyana programs. In this step we start from the previous coordinates and we perform an energies minimization within NMR restraints and adding electrostatic and/or solvents contributes using a Molecular Dynamics program; in this case Amber.
Convert pdb file from Cyana to Xplor-nih format using web-enmr utilities -> Convert pdb….
Create psf topology using site utilities -> Random Structure generation from sequence.
Upload pdb sequence file. Untar the resulting file and take protein.psf file.
Covert the cyana UPL format to Xplor-NIH format using web converter -> upl to tbl
Open the output zip and extract the .tbl file
In rdc.tbl substitute all resid 999 with resid 501. This is the xplor-NIH tensor associated to the RDC.
Open Calculation -> Amber structure refinements
If there is no one already present, create a Project, and press “new calculation”.
Fill the fields in the form following the same schema as in the previous example
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Submit the job:
Click retrieve and then analyze the output as in the previous calculation