Filing - Science topic

Has anyone found a solution for the issue with this?

Hi Alfonso, and thank you for your suggestion! No, I didn't use this option before, it was always off. Surprisingly, if I toggle this option on, FIJI can't open a large 3D stack ND2 file ("Unsupported file format or file not found").

just take the fasta sequence from both files and perform homology modelling. you can't merge two pdb files together.

Hi

I am also working on PWCOND and here is y published work.

1.

2.

I can tell u some of these.

pls send me the input file.

Muhammad Saleem

Hi Hamed Zahraee, since I have been renting out the server to run the simulations as I don't have the resources, I am afraid I won't be able to run a longer simulation as the rental period is over.

Do you have any other suggestions? Thank you.

Whoops! Looks like researchgate doesn't like me posting a link!

is the intendedlink not just the generic cambridge webpage!

Hi Chelsea St. Germain,

Did you overcome this issue? I also got this problem even with the files that were previously successfully analyzed.

Best,

Alex

It was the commercial 18.2 that had the error. Thanks

Hello all,

I appreciate the responses.

I managed to find a solution on Linux using Wine (though not specifically version for Linux yet).

All is well.

Thanks once more,

Abdelmalek

hello sir please if you fined the answer could you help me i have the same issue

Dear Rainer Thomas. Yes I have this very nice paper. Please contact me.

Sincerely P. Bouvier

Thank you very much. Pierre Caulet

For the goemetry export/import igs or step is a good format. You can easiky make an export from tekla and ten import it to abaqus.

An efficient approach to processing BrainVision files with ECG data in EEGLAB involves the following steps: Download and set up EEGLAB along with the necessary plugins: Make sure that you have MATLAB installed and the EEGLAB toolbox. Furthermore, in order to properly use EEGLAB, you must install the BIOSIG plugin, which can handle several electrophysiological data types, such as BrainVision files. To do this, use the "File" menu and choose "Manage EEGLAB Extensions." Then, proceed to install the BIOSIG plugin. Import the BrainVision file: BrainVision data files have three components: .vhdr (header), .vmrk (markers), and .eeg (binary data). To import these files into EEGLAB: Launch the EEGLAB software from the MATLAB command line using the " eeglab " command. Navigate to the "File" menu and choose "Import data." From the dropdown menu, choose "From other formats using BIOSIG." Choose the .vhdr file that corresponds to your dataset. Perform ECG data identification and preprocessing. After being loaded, the EEG dataset will be shown in EEGLAB. You focus on working with ECG data, be sure you locate the appropriate channel(s). While the specific naming practices may differ, ECG channels are often designated. If needed, the ECG data may be preprocessed using filters, detrending, or other preprocessing techniques. For example, powerline noise may be eliminated by using a notch filter, or the signal can be smoothed using a low-pass filter. Analysis and treatment of artifacts: ECG signals may include several types of noise and artifacts. To manage artifacts, it is advisable to use the built-in tools or extra plugins in EEGLAB. One may use independent component analysis (ICA) to distinguish and isolate noise or artifacts from the ECG signal. To perform heart rate variability analysis or identify certain ECG characteristics, such as R-peaks, it may be necessary to develop bespoke scripts or use specialist toolboxes. Exporting or doing more analysis: After the data has been cleaned and preprocessed, it may be exported for further analysis or visualization. To facilitate its use in other toolboxes or programming environments, you may export it as a MATLAB matrix using commands such as eeg_getdatact().

Hello dear Sara Dzhabieva

Make sure that your computer or computational cluster has enough available resources to accommodate the requested number of processors. This includes checking the total number of available CPU cores, memory (RAM), and any other system requirements for running Gaussian calculations. Ensure that your Gaussian license permits the use of more than four processors. Some Gaussian licenses may have limitations on the maximum number of processors that can be used simultaneously.

Another suggestion is the MolQube.com specialized team, whose activity is specialized in the field of computational chemistry. Give them an email: [email protected]

I got the same issue too! Anyone knows what's the problem? My input file is as follows:

%chk=C:\G16W\Testing_file\Foraldehyde energy.chk

# apfd/6-311+g(2d,p) geom=connectivity

Formaldehyde energy

0 1

C 0.00000000 0.00000000 -0.56301626

H 0.00000000 -0.92697196 -1.09694672

H -0.00000000 0.92697196 -1.09694672

O 0.00000000 -0.00000000 0.69656515

1 2 1.0 3 1.0 4 2.0

2

3

4

The KMLYP functional is not known to me, the BHHLYP seems to be called BHandHLYP in the Gaussian. You can find all the details about DFT functionals implemented within the Gaussian there https://gaussian.com/dft/

Is your file larger than 80 MB? This seems to be the limit of file size. See the last reply by Giacinto Libertini in https://www.researchgate.net/post/Error_accepting_a_file_How_can_I_solve_this_problem.

How did you decide how many ions to pack in a simulation box ?

You can use spaCy NER (named entity recognition models) or hugging face transformers, depending on the topic each model is trained to detect.

Hope it helps,

Az

Hello Akash Jena See these links

Jobin Thomas this is the pdbqt file of the docked protein-ligand complex.

If you are certain your projections are correct, you can use dis_conv_tol to reduce the convergence threshold

You could try using moltemplate.

Hi ,

i want to have mobility for LoRaGW. did you find solution for solve it or not?

i would be very grateful if you could help me.

Already PDF. I would NEVER post a MS Word file. It's large, but that is not the problem. I have tracked the issue to two PDF files which were subsets of the single consolidated file I created. These are error-free PDFs (afaik) which open fine in Adobe Acrobat Reader without complaints. But if uploaded to Research Gate the system abandons them without diagnostics or error messages. Simply hangs for a long time and abandons. Same effect with SMALL files on their own.

Dana Alexander,

The best way is to convert your data into edf. format. That definitely can help you import all files, and then create one study.

To split vina pdbqt file -You can use this command:

"C:\Program Files (x86)\The Scripps Research Institute\Vina\vina_split.exe" --input output_outfile.pdbqt

You wrote 'config. txt' but it should read 'config.txt'.

HELLO,

Please, How can i download Anura3D?

Best regards,

Rania BEN HMIDA

I also met this question, I dont know what to do

Thank you for your information

The etching of the circled part is to prevent a short circuit. The contacts must be formed such that the edge of the metal is away from the edge of the other layers. Instead of etching the FTO you can also protect the edges by using adhesive tape that can be lift-off after depositing the Ag.

Another CFD test case (ISAAC by Joseph H. Morrison). The elapsed times are 10.25 and 4.78 seconds.

IYH Dear Ancy G C

That's some old software :D

OK, here is a 1990 manual on Borland Turbo Profiler https://doc.lagout.org/science/0_Computer%20Science/0_Computer%20History/old-hardware/borland/turbo_assembler/Turbo_Profiler_1.0_Users_Guide_1990.pdf

If you have some tech savvy and the right emulated environment you can likely run the Borland Profile software and read your files. The sw can be found here https://archive.org/details/borland-turbo-debugger-profiler-assembler

Ariha Zaid your ligand files are not prepared, so I will suggest you to please prepare your mol2 files and then upload in swiss PARAM server

Providing the example simulation input file for Materials Studio is essential for reproducibility and transparency in scientific research. Here's a step-by-step guide on how to do it:

1. **Identify the Input File**: Locate the input file you used for your simulation in Materials Studio. Typically, these files have extensions like `.xsd`, `.inp`, or `.castep`.

2. **Document the Input Parameters**: Create a document or a section within your article where you list all the input parameters used in your simulation. Include details such as atomic coordinates, lattice parameters, simulation conditions, and any other relevant settings.

3. **Prepare the Input File**: Before sharing the input file, ensure that it doesn't contain any sensitive information or proprietary data. Remove any sections that are not relevant to the simulation you're presenting.

4. **Provide Instructions**: Write clear instructions for how to use the input file. Explain any special considerations or dependencies required for running the simulation.

5. **Include in Supplementary Material**: When submitting your article, include the input file as part of the supplementary material. Make sure it's clearly labeled and easily accessible to reviewers and readers.

6. **Version Control**: If your simulation involves multiple steps or iterations, consider providing multiple versions of the input file to demonstrate the progression of your research.

7. **Check with Journal Guidelines**: Some journals may have specific requirements for sharing simulation input files. Make sure to check their guidelines and comply with any formatting or submission instructions they provide.

8. **Open Data Repositories**: Consider depositing your input files in open data repositories or platforms like Figshare, Zenodo, or your institution's repository. This ensures long-term accessibility and helps other researchers validate your results.

9. **Collaborate with Experts**: If you're unsure about preparing the input file, seek assistance from colleagues or experts familiar with Materials Studio or computational materials science. They can provide valuable insights and ensure the accuracy and completeness of your input file.

By following these steps, you can effectively provide the example simulation input file for Materials Studio and address the reviewers' request in your article submission.

This channel may help you

The version of Python you are using has a memory leak and is therefore not compatible with the Autodock4.py script. Somehow the version of Python you have consumes all the memory on your machine when you run Autodock4.py, you have to fix that first before trying to continue with Docking.

Are you using Windows? You can try reinstalling python on your machine or if not, you can use WSL and try to run everything from there.

Good luck!

Hi,

basically you can not use pdb2gmx (only works for Proteins, DNA/RNA and some cofactors). You must 1) generate the modified system manually, or 2) generate two topologies and mannualy join them. When I have to generate such topologies, I use AmberTools to get the system and then convert it to GROMACS using ParMed.

Dear Faruque,

Thanks for your response. could you be kind enough to elaborate your response, please

Hi Protsan

At the end of the input (in the text file), press enter twice and write the name of the file (for example: input.wfn). Enter the keyword output=wfn in the command line.

Note, the volume of generated files is sometimes large and requires powerful systems. I use MolQube.com servers. They prepare the input according to your opinion, run the calculations and extract the data you need. You can contact them by email. email:

Binding energy is a pretty broad term and I believe spin polarization requires a special DFT method. Free energy and other thermal corrections should be present in a normally terminated frequency output.

I need help with this too

Guhyeon Jeong An orthorhombic CsPbBr₃ JCPDS file is attached.

I really hope this is useful to you.

Warm regards,

Alvena Shahid

Check the Mplus website or documentation to see if there are any known compatibility issues with Mac Sonoma updates. Software developers may provide information or updates to resolve issues.

Try reinstalling the Mplus software to see if this solves the problem. Sometimes the update can cause problems with existing software installations.

Make sure your Mac is updated with the latest Sonoma updates. Compatibility issues can sometimes be resolved through Apple's own software updates.

Find a forum online or contact Mplus support team. Other users may have encountered similar problems and may find solutions that may help you.

Consider contacting the Mplus vendor directly to report the issue and see if they can provide guidance or software updates to resolve the issue.

thank you so much

you can convert h5a to rds by using anndata library.

you can use this script to install it:

pip install anndata rpy2

You can first convert the "ATCG" hapmap format of your file to numerical genotypes format in TASSEL. Then simply write an appropriate scrip in to convert into the -1/0/1.

For example, here is how I convert my file from the 0/1/2 to 1/0/-1

file[file== "0"]<--1

file[file== "1"] <-0

file[file== "2"]<-1

You have to be careful the orders during conversion.

Dear all,

I am looking for a robust software to dock three protein molecules? I could not do it through Cluspro? Thank you.

XCMS online remains the standard tool.

I had the same problem, just tried another day and worked.

Have you solved this problem ?

I'm thinking about the way is running the code with commandpromt:

mcnp6 z RUNtpe=(file name) COM=(command file name)

Hello Ma. Flynne Dagalea.

I don't have access to JCPDS cards, but I can compare the obtained pattern with Crystallographic information files (CIFs) deposited in crystallographic databases, by using Rietveld Refinement method. It gets the same effect as compare with a JCPDS card, but if you really need this card, there are people around that will came up with what you need. Let me know if you want to do a Rietveld refinement, I can help with this.

Best regards,

Ricardo Tadeu

Roberto D'Agosta many thanks your valuable comment. I understand. You have been very helpful! Many thanks...

That's not a great graph, because it uses a thick bar to show means and a detonator to show standard errors. It does not give any actual information about how much data you had or how they were distributed. The two strange values for group D are not evident. And the asterisk is a bit of a mystery.

What is your hypothesis? Then maybe someone can help with a recommendation for testing. Since your groups differ by dosage, it would make more sense to see if the observed values are a function of dose, rather than treating each group as a distinct treatment. This gives you a directional hypothesis, and a lot more statistial power.

Hi Jun Zhang , check this question and subsequent answers. I think this will solve your "problem". Kind Regards

Rob

Salam and Hi to all, I want to learn on how to process and interpret GPR data, can anyone give suggestion which the best articles etc.?

Question

Can I ask how to get the reference to calculate the IFU/ml from GV value?

Thank you very much for your response, Wolfgang. With best regards, Javier.

See also https://www.researchgate.net/post/Error_accepting_a_file_How_can_I_solve_this_problem for a similar case. There seems to be a file size limit.

sorry u have to translate to make me understand. My majoring is on Constitution. Tq

Josie Levey

The error message "Parse error on line 1 in file '2jgd_DOCK.pdbqt" indicates an unknown or inappropriate tag. Please verify that the '2jgd_DOCK.pdbqt' file is formatted correctly to resolve this issue. You can use a tool like Open Babel to convert your files to the proper format or manually compare the errors in the Autodock Vina documentation.

To resolve the error message "mv: cannot stat 'ligand*.pdbqt': No such file or directory," please confirm that the ligand file ('ligand.pdbqt') is located in the directory where you are executing the command. If the file is in a different directory, move it to the right place or specify the correct path in your command.

Happy Docking!!

Please follow the link: https://www.compchems.com/hydrogen-bond-analysis-with-vmd/

Hope it'll help.

Compressing the file to a size of approximately <80 MB appears to resolve the problem.

But ResearchGate should indicate the limits on the size of the files that can be uploaded!

Thank you a lot!

Study about webscrapping to get better idea for what you are looking.

For which period are you running this met data: I can see on your files is from start_date = '2017-07-01_00:00:00' to end_date = '2017-07-14_18:00:00'. check weather met data are in good format. or weather you are using default settings_ Or contact me for further support: inbox me

Dear Haobam Samananda Singh

Thank you very much for sharing your file.

Best regards,

Hey there الاء علي! So, getting the structure of B36N36 and graphene Gaussian files is pretty straightforward. If you're looking to visualize them, you الاء علي have a couple of options.

For the structure of B36N36 and graphene Gaussian files, you'll first need to run Gaussian calculations on these molecules to generate the necessary output files. Once you الاء علي have the output files (typically with a .log extension), you الاء علي can extract the molecular structure information from them.

One way to do this is by using visualization software like Avogadro or VMD. These tools allow you الاء علي to open Gaussian output files and visualize the molecular structures in 3D.

Alternatively, if you're comfortable with scripting, you الاء علي can use Python with libraries like NumPy and Matplotlib to parse the Gaussian output files and plot the molecular structures yourself. This gives you الاء علي more flexibility and control over the visualization process.

So, depending on your preference and familiarity with software tools, you الاء علي can choose the method that suits you الاء علي best. If you الاء علي need more detailed instructions on any of these steps, feel free to ask!

Terrible mix up between classical and

Quantum physics.

Hi. For the case of orthorhombic structures where you create as you say three input files (each one varying a,b,c), just take the resulting volumes of each input file and also the total energies. Then create an .in (with the emacs command, for example) where your first column is the unit-cell volume (in u.a^3) and the second the total energy (in Ry, for example). Then load it in QE and use the ev.x command as shown in the example:

#comments

ev.x

Lattice parameter or Volume are in (au, Ang) > au #You are asked for the units

Enter type of bravais lattice (fcc, bcc, sc, noncubic) > noncubic #Orthorhombic structure is noncubic

Enter type of equation of state :

1=birch1, 2=birch2, 3=keane, 4=murnaghan > 4 #depends on what you choose.

Input file > .in #enter your input with its name

Minimization succeeded

Output file > .out #you are asked to enter a name for your .out

Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL

I hope I understood your question to answer it satisfactorily.

Vipul Kumar Ambasta so these parameters were adjusted for cubic symmetry. Maybe this vesta emage can be arise from these parameters. I am not sure