[chimerax-users] protonation of small molecule

[Elaine Meng]

Hello,
You would have to examine them individually on a case-by-case basis.  There is no single answer or command option that will fix everything.  In some cases (but not always) you could try to fix by removing hydrogens and then changing the atom type assignments (with setattr command and attribute idatm_type), and then re-adding hydrogens.  However, there may be some unusual functional groups like isothiocyanate (etc.) that you may not be able to handle with the available atom types.

This case-by-case examination would have be done interactively.  

Example, pretending that in this small molecule I want to make the R2-C=O (atom types C2, O2) into R2-C(H)OH instead (atom types C3,O3), :

open pubchem:12123
delete H
label #1 atoms attribute idatm_type

... hovering the mouse over the atoms I can see the atom names are C7 and O1.  I could select one by one and use "sel" in the setattr commands, but instead I'll just use their names.

setattr @c7 atoms idatm_type C3
setattr @o1 atoms idatm_type O3
addh

See setattr
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/setattr.html>
atom attributes
<https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html#atom>
atom types
<https://rbvi.ucsf.edu/chimerax/docs/user/atomtypes.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 Sep 5, 2022, at 7:36 AM, Enrico Martinez via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Dear ChimeraX users!
> I need to protonate a small molecule from the input pdb file producing
> another pdb with the protonated ligand.
> 
> I use the following batch script:
> 
> open 'ligand_without_H.pdb'
> addh hbond false
> save ligand_with_H.pdb displayedOnly true
> exit
> 
> Depending on the complexity of the input 3D structure of the ligand
> some protons could not be added so the final protonation state is not
> correct. Is there a possible way to fix this issue?
> Many thanks in advance
> Enrico