[Chimera-users] substituting atoms

simon chapman rowanlodge19 at gmail.com
Mon Jan 1 13:15:01 PST 2018

Very kind Elaine.Many thanks.  I found a route to atomic substitution after
a bit of tinkering. Tools>structure edit>build structure>modify structure.
I'm getting some great data now! Very pleased.

I will try your suggestions re extending the run-time. I don't really need
anything more than a few ps at moment: my hypothesis is that a guanine
quadruplex will be destabilised by incremental substitution at O6. So far
the data are going my way!

AMBER gave me real headaches...I have it set up in UBUNTU but on a Win10
machine, and the commands get a bit 'sticky'. It rather feels like the
package has been poorly ported into UBUNTU in several stages over a long
period by different designers. Also an over-detailed guide doesn't help.
GROMACS is another LINUX-based system. NAMD works reasonably well, but
Chimera tops the list so far. It will be a subsection of my dissertation.

Best wishes   Simon

(Looks like you and I are the only folk working on New Year's Day!)

On 1 January 2018 at 19:33, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Simon,
> The calculation runs on your own computer and as far as I know, there
> isn’t a limit on the run time.  The  “Run Parameters” section of the
> Molecular Dynamics SImulation dialog allows you to enter the numbers of
> steps for minimization, equilibration, and production.  If you click on
> “minimization” you can see it is actually a little a menu that can switch
> to “equilibration” and “production” subsections.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html#run>
> You can also specify a restart file for the production run, for
> subsequently doing another production run starting from the endpoint of the
> current one.  As far as I know, there isn’t an upper limit to the number of
> steps per run, but it might be wiser to do multiple production runs anyway
> (so that if something happens, you don’t lose so much prior computation).
> The tool was intended more to make MD simulations accessible to many
> people without too steep of a learning curve, rather than for very
> large-scale, long simulations which might be accomplished more efficiently
> with a dedicated MD package (AMBER, GROMACS, etc.), but you can certainly
> try.
> 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 30, 2017, at 4:10 AM, simon chapman <rowanlodge19 at gmail.com>
> wrote:
> >
> > 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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