simtk.org

Hi Gunnar,
first of all, direx is great!
It would be even greater if it could also deal with iron-sulphur clusters and small molecules like Mg or nucleotides.
Is this possible or do I have to erase the density for the molecules before using direx.
MfG,
Stephan

Hi Stephan,

in general DireX should be able to deal with all kinds of ligands and ions, etc. It will however assign standard parameters (like van-der-Waals radii) to those atoms that it does not recognize. This could lead to some local distortions, which you could try to correct by a final optimization with some other MD/molecular mechanics program.

For the iron-sulfur cluster you might need to define manually distance restraints to maintain the correct coordination.

Let me know how this goes, if you have any trouble with a specific ligand, I can try to fix this.

Gunnar