[Chimera-users] Dockprep OT2 C terminal question

[Elaine Meng]

Dear D.
It is impossible to answer since I don’t know what OT2 is… it’s not a residue name in the RCSB PDB database.  You would have to attach an example file.  Maybe you mean it is just one atom added to make a C-terminal carboxylate.  In that case you could try editing the file to make it have the same residue name and residue number as rest of the end residue, with atom name OXT (the other carboxylate oxygen is just named O).  If it’s some other nonstandard residue with multiple atoms, then it should automatically go through Antechamber charge calculations when you use Add Charge.  If the default method of charge calculation fails you could try the simpler Gasteiger method instead.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge.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 16, 2019, at 5:11 AM, Danilo Boškovic <a01406823 at unet.univie.ac.at> wrote:
> 
> Dear caretakers,
> 
> I have a non-standard residue OT2 (C terminus last O atom) that does not get recognized in the amber force field (everything else is fine). How do i rename this residue so it is properly accounted when adding charge?
> 
> Sincerely,
> 
> D. Boskovic