[Chimera-users] Blank screen after MD simulations

[Elaine Meng]

Any of those programs mentioned previously could be used to generate a molecular dynamics (MD) trajectory, and then you can use different tools (including Chimera, but there are many others too) to analyze the MD output trajectory:  i.e. to play it back, take measurements and plot them, etc.

We are not experts on those MD programs, but each one has its own details of how you would run the calculation, and how you would define parameters for that substrate molecule, and what other programs could be used to analyze the results.  Probably the most important thing is which program you can figure out how to install and run on your system.  I don't know which are easier to learn than others.  You might look up their websites and see if they have tutorials for similar situations as yours.

Below are a couple of web servers to get parameters for small organic molecules (maybe your substrate), but I haven't used them myself so can't help further:

SwissParam provides topology and parameters for small organic molecules compatible with the CHARMM all atoms force field, for use with CHARMM and GROMACS.
<https://swissparam.ch/>

LigParGen provides force field (FF) parameters for organic molecules or ligands up to 200 atoms, gives parameter and topology files for commonly used molecular dynamics and Monte Carlo packages OpenMM, Gromacs, NAMD, CHARMM, LAMMPS, TINKER, CNS/X-PLOR, Q, DESMOND, BOSS and MCPRO.
<http://zarbi.chem.yale.edu/ligpargen/>

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 28, 2021, at 7:28 AM, Sri Oruganty via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> 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
> 
> 
> 
> 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
>> 
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