[Chimera-users] Blank screen after MD simulations

Sri Oruganty sri.oruganty at gmail.com
Tue Dec 28 07:28:12 PST 2021

Hi Mr. Pettersen,

I am trying to analyze how an enzyme will interact with a new substrate
that it is introduced to. Do you happen to know what software you suggested
would be best for that analysis?
Best regards,
Srigouri Oruganty
Pronouns: She, her, hers
sri.oruganty at gmail.com

On Mon, Dec 27, 2021 at 5:39 PM Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Hi Srigouri,
> The black frames are typically symptomatic of a system that "blew up",
> i.e. some atoms were not correctly parameterized and consequently wound up
> directly on top of one another during the simulation, which results in an
> infinite energy and immediately thereafter coordinates that go to infinity;
> hence the black frames.
> Chimera and the Molecular Modeling Toolkit (MMTK) that it employs can
> always correctly parameterize standard amino and nucleic acids (and water),
> so it would be other molecules in your system that are producing the
> parameterization problem.  If these other molecules are not important to
> your reason for running the simulation, you could simply delete them before
> beginning the entire MD process.
> If they are important, then you would have to use a more expert-level
> simulation package in order to develop the proper set of parameters and run
> your simulation -- which will be quite challenging.  Some example
> simulation packages include Amber, Gromacs, Namd, Charmm, and OpenMM.
> --Eric
> Eric Pettersen
> UCSF Computer Graphics Lab
> On Dec 26, 2021, at 8:48 AM, Sri Oruganty via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> Hello,
> I am a senior in high school, and I was interested in learning about
> proteins and mutations. I download Chimera to run MD simulations on a
> specific protein, but not all the frames are loading. After the frame
> number gets to a certain point (i.e. 14) every subsequent frame is
> completely blank. Why is this happening?
> Best regards,
> Srigouri Oruganty
> Pronouns: She, her, hers
> sri.oruganty at gmail.com
> (610)-207-6325
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