[Chimera-users] substituting atoms

simon chapman rowanlodge19 at gmail.com
Tue Jan 9 01:30:38 PST 2018


Hello Elaine, sorry to bother you again.

Chimera has been a real treat so far, but I have hit a problem. I've
struggled for a week now, and finally given up!

I am incrementally substituting S for O on four guanines in a regular
complex. 3 substitutions work fine in a simulation and producing very
encouraging data (attachment 1) But 4 substitutions (attachment 2) triggers
a load of error messages. The first is attachment 3. After solvation,
attachment 4 appears and the solvation box is removed if neutralising ions
are added. If ions not added, attachment 5 warning appears.  Not sure if
attachment 6 is relevant.

Hope you can help/advise?

Best wishes   Simon

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
> >
> >
> > _______________________________________________
> > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> > Manage subscription: http://plato.cgl.ucsf.edu/
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>
>
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