[Chimera-users] R: Minimization on complex

[Francesca Magarotto - francesca.magarotto2@studio.unibo.it]

Thank you really much
________________________________
Da: Elaine Meng <meng at cgl.ucsf.edu>
Inviato: domenica 28 novembre 2021 20:22
A: Francesca Magarotto - francesca.magarotto2 at studio.unibo.it <francesca.magarotto2 at studio.unibo.it>
Cc: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
Oggetto: Re: [Chimera-users] Minimization on complex

Hi Francesca,
There are different ways you could do it, but personally I would:

(1) Combine ligand and receptor into one model.

T o combine the ligand and the protein into one model, you can use the Model Panel (open from Favorites menu) "copy/combine" function.  You have to choose the two models (the ligand and the protein) on the left side of the Model Panel and then click "copy/combine" button on the right side of the Model Panel.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#chosen>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#combine>

Or, instead of Model Panel, you could use the "combine" command.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html>

(2) Close the original two models so that only the new combined model is open.  Save PDB of the new combined model.
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>

You don't absolutely have to save a PDB file at this point, but you should always save your work frequently.  Some reasons:
(A) if some later step gets messed up, you can start over by opening this PDB file again.
(B) if  you decide to use some other program for later steps you can open the PDB file in that other program.
(C) saving a file before minimization allows you to easily compare with the structure after minimization

(3) dock prep, minimize, and probably save another PDB.  There are minimize options for only allowing selected atoms to move ("fixed atoms" cannot move), so that's how you would limit the movements to hydrogens.
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 27, 2021, at 1:01 AM, Francesca Magarotto - francesca.magarotto2--- via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>
> Hi,
> 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,
> thanks.

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