I am uploading 20 ensembles in the single PDB file, after energy minimization I just got one PDB structure. Is there any possibility to get 20 ensembles out?
Only your first model was likely minimized. Easiest is to do this separately.
At present, it is my understanding that YASARA does not have an automated way of doing sequential energy minimizations on an ensemble of protein structures, such as a multi-model PDB file from an NMR solution structure determination. However, you could use OpenBabel to split the ensemble into separate files (PDB or other file formats) and then manually load these sequentially into YASARA for energy minimization.
For example, suppose you had the NMR solution structure file, 2yrb.pdb. Then, from the command line with OpenBabel installed:
obabel 2yrb.pdb -O 2yrb.pdb -m
The output would be separate pdb files, 2yrb1, 2yrb2, ....
If you have access to CCG MOE, you could import the 20 pdb files into a MOE database and then in the database viewer, do Compute > Molecule > Energy Minimize. MOE will then step through each structure doing an energy minimization according to the parameters that you set for the force field and minimization algorithm.
You might also wish to contact YASARA tech support and request this feature to be added to the program. Alternatively, you could write a YASARA macro to do the job.
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