Filing - Science topic

I am trying to run a md stimulation in gromacs for HDAC2 inhibitor and ligand. The protein is metalo protein, contain a Zn atom. Now I am facing problem whille running the nvt.mdp file. I have attached the error details. It will be very helpful if anyone can solve this error.

Hi All,

I am trying to use SAMOVA 2.0 on 68 populations comprised of two interspersed species and I keep getting "No vertex found for a bisector". I have checked the SAMOVA2.log file and the groups are found "geographically homogeneous". I cant figure out what this error means and is especially confusing since I can perform the analysis on each species individually with no issues.

Has anyone come across an issue like this before? I haven't been able to find anything regarding software limitations, such as number of populations. Any help or advice would will be greatly appreciated.

Thanks for your time,

Dan

Hello to everyone,

I am trying to launch a BLYP optimization with ORCA starting from an already converged calculation at BP level ,exploiting its orbitals and geometry as a guess.

I tried several combination of the keywords Moread,MOinp and guessmatrix cmatrix but nothing seems to work.

I also tried to launch the calculation replacing manually the converged geometry in the input file, but it doesn't work , it always say the it can't open the converged geometry file or that is trying to read from a general file but it stops there.Even if the file is in the same folder.

Could you suggest me an example? Because the on that i found on the manual are not working.

Here is my input

! BLYP D3 def2-TZVP opt def2/J miniprint nopop SlowConv

%scf

Guess MOREAD

MOInp "Au84.gbw"

guessmatrix Cmatrix

MaxIter 800

AutoStart true

end

%maxcore 5300

%pal nprocs 36

end

* xyzfile 0 1 Au84.xyz

these are the slurm errors

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

!!! FATAL ERROR ENCOUNTERED !!!

!!! ----------------------- !!!

!!! CANNOT OPEN FILE !!!

!!! Filename: Au84.xyz !!!

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

!!! FATAL ERROR ENCOUNTERED !!!

!!! ----------------------- !!!

!!! CANNOT OPEN FILE !!!

!!! Filename: !!!

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

Thank you in advance

During molecular dynamics, I'm facing the error mentioned above. How can we fix it, I checked the lig.prm file to see if it is missing some angle parameters but it doesn't seem so, the file is attached below. If anyone can help to find the error and fix it would be appreciated.

Thanks in advance

Regards,

Vinay

In dental applications, virtual models obtained from the patient's mouth using intraoral scanners are unfortunately saved in STL format. However, when a solid model is needed, the stl. file format is inadequate, and the step. file format becomes essential.

Hi, All!

There is a dataset including about 10000 samples which is a beta-globin gene cluster genetic variant report for every sample(part of a report uploaded). Is there any tool recommended to convert it to a Variant Call Format(vcf) format?

We are willing to make notice of Miller indices present in XRD powder and managed as their JCPDS files. We need them for various substances, e.g. Graphite, copper, lithium, and Iron. Kindly share me the JCPDS database files of these elements. Best regards and thank you very much for your help and guidance.

I made a series of jump tests in subjects, everything was recorded with Vicon. I have data from markers and force plate. We recorded the tests before and after an intervention.

My question is, I have C3D files with the markers and force plate, I want to mount the files before and after an intervention side by side, and synchronize them, then export this as an video file, it can be in any format.

What would be the easiest software to do this?

I am looking for resources in the Netherlands regarding cultural tourism. So what cultural activities correlate, and what lifestyles can be distinguished. Any resource is welcome, articles, factor analyses, correlation matrices, spss files etc.

what is the keyword to add omegaB97X functional in gaussian input file?

How mat I export in a Tab-delimited (win) file?

I am working on a molecular dynamics simulation in protein-ligand system, using NAMD software, and I got the following error.

"FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HGA1 CG3C51 SG311 (ATOMS 1753 1752 1770)"

The atoms mentioned above belong to the ligand structure. The .str and topology files for the ligand were generated using Charmm-gui. Can someone help me to solve this failure? Thank you in advance.

Hello there. Several references say that there is a reader for .sav files from SPSS in Weka, but I just can´t find it. Can anyone provide help? Thanks in advance

Is there any script that reads the GAMESS frequencies.log file and get the distortion geometries along the frequencies modes?

Article A scoping review on Covid 19 and gender based violence: a child marriage based study in Africa

Authors T Mabemba, UP Ejoke, HN Ntombela, ED Du Plessis

Gender and Behaviour, 2023

I was uploading the file and it refuses. I think because it starts with HN Ntombela and I am registered on researchgate as Ngenisiwe Ntombela not with initials.

How can I do to upload this article in my name as co-author.

Regards

Ngenisiwe Henrietta Ntombela

Hi all,

I have citation information in CSV file format which I want to convert into BIB file format to be used on Biblioshiny application for the systematic review writing.

Actually, I tried to load a CIF file in the Crystal Explorer Software. But shows error like "Error Processing CIF - There is an error in the Tonto stdout file, and no data has been loaded. The stdout file will be shown for inspection (Screenshot Attached)." Kindly help me to rectify this problem. Thanks in advance.

Hello everyone,

I am facing a problem when making a plot in "R". I am generating a ROC curve, but in the graph I have been oberving that my "0.0" scale of of X-axis is far from "0.0" scale of Y-axis. I don't understand where is problem. I want to make the plot where "0.0" will start from the same point. I am giving you the example of what I found from R (Please check figure of R) and also what I want (Like figure drawn by GraphPad)

If anyone please help me to find the solution, I will be highly benefited. I am providing the script that I use.

# Install and load necessary packages

install.packages("pROC")

# install.packages("readxl")

library(pROC)

library(readxl)

# Read data from Excel file (replace with your file path)

data <- read_excel("D:\\Samsun medical center\\ELISA data analysis\\elisadata\\New prism analysis for AUC curve analysis\\Sample data for R.xlsx")

# Extract control and cancer patient data

control <- data$Control

cancer <- data$Cancer

# Combine data and create a grouping variable

data_combined <- c(control, cancer)

group <- factor(c(rep("Control", length(control)), rep("Cancer", length(cancer))))

# Create ROC curve

roc_data <- roc(group, data_combined)

# Plot ROC curve

plot(roc_data, main = "ROC Curve", col = c("blue", "red"), legacy.axes = TRUE,

print.auc = TRUE

xlab = "100% - Specificity", ylab = "Sensitivity", asp = 1) # Set aspect ratio to 1:1

# Calculate AUC with confidence interval

auc_value <- auc(roc_data)

ci_value <- ci.auc(roc_data)

# Extract AUCs for control and cancer groups

auc_control <- roc_data$aucs[group == "Control"]

auc_cancer <- roc_data$aucs[group == "Cancer"]

# Perform Mann-Whitney U test to compare AUCs

p_value <- wilcox.test(auc_control, auc_cancer, alternative = "greater")$p.value

# Display AUC, CI, and p-value on the plot

legend("bottomright",

legend = paste("AUC =", round(auc_value, 2),

"\n95% CI =", round(ci_value[1], 2), "-", round(ci_value[3], 2),

"\np-value =", signif(p_value, 3)),

bty = "n")

# Calculate Youden's Index

youden_index <- roc_data$thresholds[which.max(roc_data$sensitivities + roc_data$specificities - 1)]

cat("Youden's Index Cutoff:", youden_index, "\n")

# Find the index corresponding to Youden's Index

index <- which(roc_data$thresholds == youden_index)

# Extract sensitivity and specificity at Youden's Index

sensitivity_value <- roc_data$sensitivities[index]

specificity_value <- roc_data$specificities[index]

# Convert sensitivity and specificity values to percentages

sensitivity_percentage <- sensitivity_value * 100

specificity_percentage <- specificity_value * 100

# Print sensitivity and specificity values as percentages

cat("Sensitivity at Youden's Index:", sensitivity_percentage, "%\n")

cat("Specificity at Youden's Index:", specificity_percentage, "%\n")

I want to extract mid-latitude, high-latitude, equatorial region from ionex winrar archive file. I need the script.

i want to calculate phonon using ph.x , qe-6.5 but i get this error.

========================================================

Error in routine read_rhog (2):

error reading file ./_ph0/prefix.q_2/prefix.save/charge-density

================================

the file created in that dir is 'charge-density.dat' and not the 'charge-density'

A slicing software (such as Cura from Ultimaker) can take a CAD file and develop the .gcode file for the toolpath. However, this might nor be compatible the with Nachi robot environment. I would like to know if there is any slicing software or programs that can convert the .gcode file to nachi program.

We use BCS-810 under BT-Lab software control. After a short time, Windows does not allow to use its copy function (text to buffer, files anywhere). Everything was consequently changed: the BT-Lab software version, the whole PC, the version of Windows from 10 to 11. Rebooting helps for a short time, but can't be frequenly done. The only fixed part was the BCS-810 device.

Has anyone encountered such a problem? How was it solved?

While docking using AutodockTools 1.5.7, this msg pops up in the command prompt while inserting protein, but grid parameter files and the binding affinity results are perfectly generated. Is it ok to continue docking with other ligands while this error(swig/python detected a memory leak of type 'bhtree *', no destructor found) shows up?

Good Morning,

I'm trying to import xyz file following tutorials but I have an error message (in the figure below). I need help

I have intel iris xe graphic card. i want to run dft calculation in gaussian using a gpu. what are the necessary modifications to the input file? my input file read like this:

%chk=gagl.chk

%mem=1gb

%nprocshared=4

# opt b3lyp/6-311+g(d,p) geom=connectivity

i tried increasing processor and memory but the program terminate

I like PCW and profex as they are free softwares. It would be great to put the cif, and str files together with my samples to better identify. I work with XRD applied to mineralogy.

Thanks!

Hello, I have some raw files which extension is .d (acquired from Brucker instrument). Which platforms would you recommend to perform the bioinformatic analysis (possibly fee downloadable)? I have experience using MaxQuant but it does not recognize the .d files. Any recommendation? Thank you in advance

please suggest CIF FILE OF ZnO

Maybe a misprint but, my PhD is on file. https://www.researchgate.net/publication/379779319_My_PhD_in_SKEPTOLOGY

Hello,

I want to get confirmation as to the correct way to specify a uniform EXTERNAL_PRESSURE in a non-orthogonal unit cell using the academic CASTEP code (i.e. not using the Materials studio interface, but rather in the generated input files).

I have a unit cell with:

a b c 8.24600 4.79900 9.19601

alpha beta gamma 90.0000 63.0282 90.0000

and I have mapped the cell to:

%BLOCK LATTICE_CART

0.0 8.24600 0.0

0.0 0.0 4.79900

8.1957587287 4.1708678686 0.0

%ENDBLOCK LATTICE_CART

The CASTEP cocumentation describes the EXTERNAL_PRESSURE block in terms of Rxx,Rxy, etc. which sounds like orthogonal Cartesians, so I am wondering : if I want to impose an isotropic external pressure of 'P' GPa, what would the EXTERNAL_PRESSURE block need to look like?

Hi I have Osirix and ICODE for anonymisation of dicom files however none do this on bulk yet.

I’m undertaking a large research project and wondered if there is something out there or something that can be coded easily, to select numerous dicom files to anonymise in a numbering order and map reports with the corresponding correct numbering convention in excel also anonymised. Thank you

I have used g_mmpbsa (rashmi kumari version) for mmpbsa study in my previous simuation. Everything was ok. But i performed three simulations on cluster having gromacs 2021. Now the .xtc and .tpr file are not accepted by g_mmpbsa. I have downloaded the new version g_mmpbsa-1.7.1 but errors are occuring in installation.

Can anyone share executable g_mmpbsa and energy2bfac files so that i can add them directly to bin and g_mmpbsa 1.7.1 can run.

Regards,

Saima Ejaz

Hello everyone

I have a query regarding md simulations

As I received CSV file for md data from my collaborators.. but the problem is in that file they did not mention the residue no for the rmsf of protein and ligand.. only time point total energy and rmsf values are given.

Can anyone help me how to find which rmsf values belongs to which residue

Thank you

Hello,

I am trying to extract the global stiffness matrix from Ansys. I am using the following command to do so:

*DMAT, MatKD, D,IMPORT, FULL, file.full, STIFF

*PRINT,MatKD, K.csv

When I open the file, I see that the matrix is printed with the index numbers as well (screenshot attached). Is there any way to print just the values? and also not have the matrix name "MatKD:" at the beginning?

I have the file, and prefer to send it privately (because I'm not a lawyer, and don't really know what permissions I have to send or post it publicly).

Please advise if possible.

Hi,

I am working on LAMMPS molecular simulation on CO2 mineralization. I have some scripts which require to compile Lammps files using cmake in ubuntu. Is there anyone who has some expertise can help me to solve that problem.

I look forward to hearing from someone. Thank you.

Sincerely,

Akash

I am looking for a way to get the number of patents granted and the number of patents filed by each listed Indian company for the past ten years. Is there any website or database that provides the same?

Hello,

I am trying to convert .mol2 file to .str file using CGENFF but unable to generate output, It showing a following error to me, can anyone help me out. How to resolve it?

Thanks,

Aadil

Dear network

I need to plot instantaneous and mean End-to-end delay in D2D and eNode-based topologies?

How to generate/visualise the accurate vec file data?

I appreciate your help

Can we process gnss data for different cutoff angles and get it as a rinex file as output?

Good day, everyone.

I am trying to create an artificial neural network with Matlab and then optimize it with the genetic algorithm. After training the network, I saved it and created the following two script files.

function fitness = fitnessFunction(x, trainedNetwork)

% Check input values

net = trainedNetwork;

if any(x < -1) || any(x > 1)

error('Input values must be between -1 and +1.');

end

try

outputs = net(x'); % use net instead of trainedNetwork

fitness = -sum(outputs); % Negative sign, since the genetic algorithm thinks it is looking for a minimum

catch ME

rethrow(ME);

end

end

%Install trainedNetwork

load('trainedNetwork.mat', 'trainedNetwork'); % Load the file where the trainedNetwork variable is saved

inputSize = 3;

% Set genetic algorithm settings

% Set lower and upper limits (between -1 and +1)

lb = -ones(1, inputSize); % Lower limit

ub = ones(1, inputSize); % Upper limit

options = optimoptions('ga', 'Display', 'iter', 'PopulationSize', 100, 'MaxGenerations', 50);

% Run the genetic algorithm

[x, fval] = ga(@(x) fitnessFunction(x, trainedNetwork), inputSize, [], [], [], [], [], lb, ub, [], options);

% Best solution and fitness value

bestInputs = x;

bestFitness = -fval; % We return it because we have marked it negative

% Calculate outputs corresponding to the best inputs

bestOutputs = trainedNetwork(bestInputs');

disp('Best inputs:');

disp(bestInputs);

disp('The highest outputs corresponding to these inputs:');

disp(bestOutputs);

When I run the second script, I get the following error.

Array indices must be positive integers or logical values.

Error in fitnessFunction (line 8)

outputs = trainedNetwork(x');

I would be very grateful if you can help me.

I have tries "a_nonSchmid_110" or "a_nS" in the material.yaml file, but none of these works. Help is highly appreciated.

Hello,

I'm writing Python scripts for Abaqus and I'm facing a problem. I need to change the coordinate system in a .odb file before extracting data but I'm stuck. I can create my coordinate system and extract the data but not the intermediate step. How can I change it using Python ? If you have any information, it would be great.

Best regards,

Benjamin Martin

The second plant in the attached file is from Monte Subasio and was denoted Inula montana. But Inula montana is the first plant photographed by me in the Alps.

My Xcrysden crashed and I was searching for the solutions. Finally, after several attempts I reached a solution of the same.

Follow these steps if your xcrysden crashes with the error "(file "/usr/share/xcrysden/Tcl/xcInit.tcl" line 633)".

Do Let me know if this works for you.

Regards,

Dr Abhinav

How can we simulate TSV in the Silvaco example?

Exactly, I need the instructions for the attachments file.

Best regards.

Hello all,

I am doing some heavy simulations in Fluent using clusters. The models are not readable by laptop or desktop because they are very heavy. So, i have to take the contours in cluster using journal file commands. But i don't know how. If anyone has experience in this field, please share it wit me. Thank you very much.

BR,

Ehsan

I need some mask for UV photolithography. Can you suggest any software to draw those patterns with proper file format so that directly the file can be inserted and required pattern can be obtained. Note I don't need PowerPoint files though we can design the mask.

the command line -----------gmx_mpi grompp -f md_pull.mdp -c eqb6.gro -p topol.top -r eqb6.gro -n new.ndx -o pull.tpr -maxwarn 3

Fatal error:

Group Protein referenced in the .mdp file was not found in the index file.

Group names must match either [moleculetype] names or custom index group

names, in which case you must supply an index file to the '-n' option

of grompp.

The default value is set as the natural abundance,how to set different levels of isotopes in the CONTROL file while using ShengBTE? Is there an example CONTROL file?

I want to calculate the lattice thermal conductivity of Bi2Te2Se. I calculated second-order Force constants using phonopy and third order force constants using Third_order.py.v.1.1.1.

But when I run ShengBTE, I am getting the following error.

At line 116 of file config.f90 (unit = 1, file = 'CONTROL')

Fortran runtime error: Cannot match namelist object name 0705

Could anyone help me to figure out this error? I have successfully run the TEST-VASP example provided with ShengBTE.

The required files are attached herewith.

Any help is highly appreciated.

check the plagiarism for the file attach below

Which file format of GSAS 2 will be supported by Origin?

Dear Researchers,

I hope this message finds you well. I am conducting PhD research in Computer Science on fetal heart rate analysis.

I am encountering difficulties in importing and using the CTU-UHB dataset (.dat files) in Python. Could you please provide guidance or a file to help  me properly utilize this dataset? Your assistance would be greatly appreciated. Thank you for your time and support.

hor can delete a wrong uploaded file ,please?

Is there any software that can take atomic positions as input (e.g. VASP POSCAR file) and give me the output of Wyckoff positions? I am trying to find vacancies of some specific Wyckoff positions from my output files.

I am working with PopArt (Population Analysis with Reticulate Trees) software making statistical parsimony haplotype networks. It uses nexus format, and I had not trouble formatting and making a single color network, but am struggling a bit with importing and applying the traits block or instruction file, my goal is to produce a network with color coded sampling regions or populations. Can anyone share an example traits file that's correctly formatted to indicate color in the network by population or geographic sampling location? Many thanks, Brenden

Currently, I want to investigate the structural, electronic, and other properties of a composite material, but have trouble in developing the necessary input file for Quantum ESPRESSO (QE). So that I am requesting assistance on how to develop the appropriate input file for QE to study the properties of the composite material. eg. ZnO/Graphene

Can anyone suggest how to design a transistor model in ansys circuit. snp file with respect to different bias is available but from the datasheet I want to design transistor and observe it's effect with respect to any bias condition.

Any suggestion would be really helpful.

In this online file you have included my last 2 publications. But your original file my (Mohammad Ansaruzzaman, student of free university Brussels & Karolinska Institute) you have included all my files.

I want to do microbiome analysis using R, for which I have three folders that contain ASV data, metadata i.e. sample data, and taxonomy data for 56 sample studies. I want to read the data in those folders and create a separate phyloseq object for each sample study, then I have to make a merged phyloseq object. The issue I am facing is that while creating a phyloseq object the ASV table is said to be non-numeric. What should I do in such a case?

I did flow cytometry experiments using guava easyCyte™ HT System and I enter an optional Sample ID for each individual well or tube.

But

When I am trying to analyse data (.FCS format) using flowJo software, I find the files are named by numbers and the date.

Could you recommend any tool to recover the sample ID?

Regards

Hi,

Attached here is the CIF file of CaCO3. I have opened it using Vesta and get the following data:

%%%%%%%%%%%

Title C Ca O3

Lattice type C

Space group name Custom

Space group number 167

Setting number 1

Lattice parameters

a b c alpha beta gamma

6.36000 6.36000 6.36000 46.1000 46.1000 46.1000

Unit-cell volume = 121.856657 Å^3

Structure parameters

x y z Occ. U Site Sym.

1 Ca Ca1 0.25000 0.25000 0.25000 1.000 0.000 2 -

2 C C1 0.00000 0.00000 0.00000 1.000 0.000 2 -

3 O O1 0.25000 -0.25000 0.00000 1.000 0.000 6 -

%%%%%%%%%%%%%%%%%%%%%%

Using the info above I have prepared the Quantum Espresso file as follows(I just point specific cards):

&SYSTEM

ibrav = 0

celldm(1) = 6.36000

/

CELL_PARAMETERS {angstrom}

6.36000 0.00000 0.00000

0.00000 6.36000 0.00000

0.00000 0.00000 6.36000

ATOMIC_POSITIONS {crystal}

Ca 0.25000 0.25000 0.25000

C 0.00000 0.00000 0.00000

O 0.25000 -0.25000 0.00000

The above info are okay? I am confused about cell_parameters how can I include alpha beta gamma angle in the QE file?

I have calculated Y2SiO5 with monoclinic system (Y1-Y2 two site, unique Si site and O1, O2, O3, O4 and O5 five site). Thus, I have used these parameters as a input file descriptions;

Monoclinic P, unique axis b

ibrav=13

celldm(2) = b/a

celldm(3)= c/a

celldm(5)=cos (ac) where beta is the angle between axis a and c

Dou you any comment for these chosen inputs

Many thanks

Dear users

I have a problem using the cppp.x postprocessing after my md calculation in quantum espresso.

Pleased find attached my inputs files. Always I got a message like this: Error reading namelist &inputpp

I started running SWAT-CUP with 100 simulations but the error message shows like in the attached screenshot that the output files does not exist in the directory path even after the calibration was run successfully.

I want to know the completeness and contamination level of bacterial genome sequence. I have the assembled FASTA file of the bacterial genome sequence.

Are there any online tools where I can upload my FASTA file and directly can find the completeness and contamination level?

Thanks in advance

Hi, I am stuck with my Amos Analysis and need help. I am unable to get any path coefficients or standardized estimates for my model. The model runs without any hassle but output file is almost empty. Every path coefficient is marked as 'Unidentified'. Seek help, please look into the attached diagram and suggest the possible reasons. Thank You.

I have a text file where includes the atomic positions of each atoms in 3D space . How to determine the Burgers vector from it?

I want to know the completeness and contamination level of bacterial genome sequence. I have the assembled FASTA file of the bacterial genome sequence.

Are there any online tools where I can upload my FASTA file and directly can find the completeness and contamination level?

Thanks in advance

I have synthesized strontium based hydroxy-apatite by co-precipitation process. i have done the rietveld refinement of it. The problem is its chi-square is not less than 2, even though I have refined them properly and zooming into each peaks after every refinement.

What can be the possible cause for this? Is it because nano-particles have been formed as a result we cant do its refinement as I read it somewhere else or is there something wrong which I have not taken care of. I have uploaded the pcr file and the image of final refinement.