[Chimera-users] substituting atoms

Elaine Meng meng at cgl.ucsf.edu
Mon Jan 1 11:33:20 PST 2018


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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