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
Heteroatoms
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Gunnar Schroeder
- Posts: 9
- Joined: Wed Mar 07, 2007 12:37 pm
RE: Heteroatoms
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
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