[Chimera-users] Query about energy minimisation

Elaine Meng meng at cgl.ucsf.edu
Sun Oct 18 09:21:41 PDT 2020

Hi Izzati,
I am very confused by your question.  

This structure already has THV in it, so why would you want to dock it??  The structure already shows where it binds.  Docking is only a guess at how something binds, so it is better just to take this structure which presumably already has the correct answer.

Secondly, even if you wanted to dock other small molecules, there is generally no reason to minimize the structure.  Minimization is not some magic way to "improve" a structure.  Generally it seems better to start with the structure that the experiments actually gave, or at least that the authors of the structure interpreted as the experimental results.

It is beyond the scope of this mailing list to explain principles of molecular modeling.  I can only suggest reading more papers (or maybe a textbook) and thinking about the logic of what you want to do.

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

> On Oct 17, 2020, at 8:29 PM, Izzati Mokthar <izzati5676 at gmail.com> wrote:
> Hi Elaine!
> Thank you for your response. I really really appreciate it. However, I still need further clarification.
> My question is I don't know how can I consider whether THV is important for my calculation. Sorry I am still new with this. After doing the energy minimisation, I will proceed with molecular docking, I need to dock THV to the protein to see the binding interaction. So, my question is should I consider that THV is important or else?
> Thank you for your time and answering my questions.
> On Sun, Oct 18, 2020, 12:13 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Izzati,
> Just like you, I can only go by what the dialog says: that there is a failure running Antechamber (the charge calculation) for residue THV.  I see it is a highly charged molecule, maybe a nucleoside diphosphate analog. The charge calculation often fails for this kind of molecule.
> What to do:
> Is the residue THV important to your calculation?  If not you could delete it before trying to minimize.  Another possibility is that when you get the Add Charge dialog (which runs Antechamber), choose the more simple charge calculation method Gasteiger.
> The bigger picture, however, is that Chimera minimization and dynamics are meant to be user-friendly and convenient, but they are relatively slow (calculation not optimized for speed) and cannot handle all situations, and do not have many options that are provided by dedicated molecular mechanics/dynamics packages such as AMBER, CHARMM, GROMOS, GROMACS, etc.  Using Chimera is not recommended if you want to do long simulations or get ANY quantitative results... instead you should use one of those other packages.  Then you can view/analyze the trajectory output from them in Chimera if you want.
> These issues and limitations are discussed in earlier posts to chimera-users:
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-September/017228.html>
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-September/017234.html>
> There are no tutorials for Chimera minimization and molecular dynamics, only the manual pages for the tools:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On Oct 17, 2020, at 8:21 AM, Izzati Mokthar <izzati5676 at gmail.com> wrote:
> > 
> > Hi,
> > 
> > I am Izzati. I have a few queries on UCSF Chimera. I need your guide to use the tools. I have two questions. Below are the questions:
> > 
> > 1.I would like to do energy minimisation for protein structure with PDB ID: 2J9F. I click Structure editing > Minimize Structure. To be honest, I don't know how to set the settings. I used the default setting and a warning pops up as the attached picture. Do you have any suggestion of reference that I can refer to, to do the energy minimisation?
> > <5.png>
> > 
> > 2. I need to also do molecular dynamics for my research. May I know whether I can use chimera to run molecular dynamics as well. If yes, where can I refer to the tutorials? 
> > 
> > Thank you in advance for your response.
> > 
> > Regards,
> > Izzati.

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