Da: Eric Pettersen <pett@cgl.ucsf.edu>
Inviato: venerdì 11 giugno 2021 22:20
A: Francesca Magarotto - francesca.magarotto2@studio.unibo.it <francesca.magarotto2@studio.unibo.it>
Cc: chimera-users@cgl.ucsf.edu <chimera-users@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

Eric Pettersen

UCSF Computer Graphics Lab

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

Hi,

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.

Francesca
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