[Chimera-users] R: Minimize hydrogens in water molecules

Francesca Magarotto - francesca.magarotto2@studio.unibo.it francesca.magarotto2 at studio.unibo.it
Fri Jun 11 13:36:49 PDT 2021

Thank you for your reply.
I've looked at them in graphic representation, but they seem complete.
Maybe there's something that I don't understand or that I'm not taking into account.
Da: Eric Pettersen <pett at cgl.ucsf.edu>
Inviato: venerdì 11 giugno 2021 22:20
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] Minimize hydrogens in water molecules

Hi Francesca,
I suggest you look at residues 393 (a GLY) and 394 (a CYS) in your structure.  I strongly suspect that one or both of them have an incomplete peptide backbone.  Minimization does not know how to deal with residues with incomplete backbones.  Your only option is to completely delete any residue with an incomplete backbone, which might not be appropriate if the residue is near the binding site.


Eric Pettersen
UCSF Computer Graphics Lab

On Jun 11, 2021, at 1:06 PM, Francesca Magarotto - francesca.magarotto2--- via Chimera-users <chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>> wrote:

I need to minimize two water molecules in the binding site of the protein: I don't want to move the oxygen, so I've selected only hydrogen atoms and then I' ve used the Minimize Structure tool (keeping fixed all atoms that are unselected).
I can't do the minimization because there's an error: Chimera/MMTK cannot minimize structure, probably because there is no parameter for ''No parameters for bond Atom 0.CYS_394__0_0_1_397__A.N (atom type n) - Atom 0.GLY_393__0_0_1_396__A.peptide.C (atom type C)''
I don't known what this means and what I should do to fix it.
I've tried to use the command line, but there's another error.
Does anyone have suggestions?
Thank you.
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