[Chimera-users] Query about energy minimisation

Izzati Mokthar izzati5676 at gmail.com
Sat Oct 17 20:29:53 PDT 2020

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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