[Chimera-users] Query about energy minimisation

[Izzati Mokthar]

Sorry for the confusion. I'll read further on this.

Thank you so much for the clarification.


On Mon, Oct 19, 2020, 12:21 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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
> -----
> 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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