[Chimera-users] substituting atoms

simon chapman rowanlodge19 at gmail.com
Sat Dec 30 04:10:02 PST 2017

Hello Elaine. Yes,remiss of me to leave out so much info! I'm new-ish  to
Chimera and wasn't really sure if there would be a reply (as has happened
with some other MD products)

So thanks for your prompt response.

I had no problems with Build Structure after being pointed in the right
direction. I will try text editor eventually just for the experience.  I
have successfully substituted S for O in a guanine complex, and will extend
that to a Se substitution later.

The MD simulation runs *much*  faster if I exclude the Periodic Boundary
Conditions option.  Is there a way to extend the run-time?  Currently  it
covers 1000fs. Is getting to picosecond region a possibility?

Best wishes and congrats to whoever put Chimera MD together!    Simon

On 28 December 2017 at 17:09, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/
> editing.html#modify>
> 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:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/
> tutorials/framepdbintro.html>
> 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.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/
> addcharge.html#antechamber>
> I hope this helps,
> Elaine
> -----
> 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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