[Chimera-users] substituting atoms

Elaine Meng meng at cgl.ucsf.edu
Thu Dec 28 09:09:06 PST 2017

Hi Simon,
It would have been helpful if you said how you substituted S for O and what the error messages were.  I have no idea what you did.  

You can change atom type and element inside of Chimera or use a text editor (not in Chimera) to change the PDB file before opening it in Chimera.  

The way to change the atom inside of Chimera is to select the atom and then use Build Structure (in menu under Tools… Structure Editing), the Modify Structure section. Use the option to change the name of the residue since if you keep the name the same, Chimera is expecting that residue, not something different with a sulphur in it.

If you try text-editing instead, remember spacing is important in PDB files, so don’t change the spacing. There's a summary of PDB format here:

In the text-editor of your choice, in the ATOM line for that atom, I would change the atom name, the element symbol (if present, would be near the end of the line), and in the ATOM lines for the whole residue, change the residue name.

Regardless of how you change the atom, however, another problem is that this nonstandard residue must be parametrized if you are going to run MD.  Chimera will try to do this automatically using AMBER’s Antechamber module, but especially with highly charged residues such as nucleotides it may fail.  In that case, I don’t really have any solution other than to try the simpler Gasteiger charges if it gives you a choice of Gasteiger or AM1-BCC.

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Dec 27, 2017, at 1:49 PM, simon chapman <rowanlodge19 at gmail.com> wrote:
> Hello...for my Master's dissertation, I need to substitute a sulphur atom for an oxygen in a Molecular Dynamics simulation. The run works fine with my target molecule 1KF1.pdb uploaded into Chimera, but the substituted version sends quite a few error messages and won't run. It doesn't appear to recognise the novel S atom.
> Any help would be much appreciated...I've been stuck on this for nearly a week!
> Best wishes   Simon

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