[Chimera-users] Minimization on complex

Francesca Magarotto - francesca.magarotto2@studio.unibo.it francesca.magarotto2 at studio.unibo.it
Sat Nov 27 01:01:54 PST 2021

I need an advice regarding minimization of complexes. I've performed a virtual screening and I've selected some molecules of interest. Now, I've looked for the possibile interactions in the binding site and I would like to perform a minimization moving only the hydrogen atoms in the binding site. However, I have to create a new file pdb complex formed by my protein and one molecule from VS results.
So, I opened the pdb file of the protein and the mol2 file of the molecule from the VS: now, do I need to save a pdb file of the complex and how to save it? I need the hydrogens to  move according to the ligand inside the protein and I don't know if it's possibile with both the type of saving (is it better individual MOLECULE sections or combined MOLECULE section?).
Moreover, I don't know if (for this kind of purpose) it's better first to save the complex in pdb file and then to use dockprep and minimization or use dockprep and minimization and only after saving the file of the complex. My main aim is to see if some hydrogens of the residues in the binding site move their places according to the presence of this ligand.
Hope someone can help me,
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