Hi Francesca, Run the minimization again, but when the error dialog comes up click "Report Bug" and attach your structure file to the bug report. That will allow me to investigate this problem. --Eric
On Jun 11, 2021, at 1:36 PM, Francesca Magarotto - francesca.magarotto2--- via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
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@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 <mailto: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 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
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