[Chimera-users] Coordinate bond problem

[Elaine Meng]

Hello,
The structure already looks reasonable to me.  Why do you think you need to minimize it?  Depending on where you got this structure, it may already be minimized.

The Antechamber process of assigning parameters for minimization in Chimera is meant to be simple and automatic, but it cannot handle everything. It cannot assign parameters for boron.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html#nonstandard>

The dialog where you say the boron is tetrahedral and has 4 substituents is only for purposes of hydrogen addition, and it simply indicates that no hydrogens need to be added.  It is not related to the charge calculation failure in Antechamber.  If you just un-check the option to add hydrogens in the first dialog (Dock Prep), the dialog about tetrahedral etc. will not appear.  Still, the failure in Antechamber will be the same.

If you really have to minimize it, you will have to use some other program, not Chimera.
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Aug 13, 2020, at 10:21 AM, Xelha ap <xelha_28 at hotmail.com> wrote:
> 
> Hi!
> I have had problems minimizing the structure of a molecule that contais cordination bonds. Chimera does not recognizes the bond.
> The structure is a BODIPY, and its characteristics is the coordination bond between Boron atom and one nitrogen.
> Can you help me to minimize mi structure? is there in chimera any option to select coordination bonds?
> When i tried to minimize it, i selected that the boron atom is tetrahedral and  subtituents but, with the following conditions to select dis not work for me.
> I get "Failure running ANTECHAMBER for residue UNKCheck reply log for details". I have been changed the next selections and I get the same answer.
> 
> Can you help me please?
> 
> M. en C. Xelha Araujo Padilla
> Estudiante de Doctorado del Programa de Biomedicina y Biotecnología Molecular 
> Lab. de Citopatologia Ambiental, Depto. de Morfología, 
> Escuela Nacional de Ciencias Biológicas-IPN, Zacatenco. Ciudad de México 
> Tel. +52(55) 57296300 Ext. 52399. 
> <BODIPY.pdb><BODIPYsdf.sdf>_______________________________________________
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