How to optimize geometry of nanoparticle for docking?

Hello Folks, I want to dock nano-particle like Fe2O3 in protein. I need to optimize the geometry of such nano-particle structure. Is there any online approach to assign partial charge and...

31 December 2017 6,374 6 View

How to elaborate SAVES Server output results?

04 May 2017 3,427 0 View

What's the difference between the I-TASSER and LOMETS?

Hello dear members, I want to build homology model for my target protein while using online server where the algorithm should be based on threading, because the available templates from PDB for my...

01 February 2017 1,623 2 View

Should i restraint protein and ligand in md production?

Hello folks, I want to conduct md simulation to explore the comparative stability and interaction mechanism of the reference compound (experimentally determined) and the newly screened candidate...

01 February 2017 9,253 4 View

How to ensure that whether the charge groups assigned to atoms in itp file are correct or not?

Hello, I have generated itp file for the ligand via SwissParam because I'm using CHARMm ff. I want to confirm that whether the charge groups assigned to each atom of the ligand are either correct...

10 November 2016 2,489 0 View

What's the basic criteria to select a suitable forcefield for protein-ligand complex MD simulation in gromacs?

Hello, I want to simulate my protein-lignad complex, but there is no forcefield information cited yet for this specific protein. I'm seeking the basic criteria which is taking in consideration to...

10 November 2016 933 9 View

Is there any hard and fast range for NVT and NPT to decide whether our system is equilibrated or not?

Hello, I prepared my protein-ligand complex for MD run, the average value for NVT is 299.99 which looks pretty satisfactory, but for NPT, the average value is 10.01 which is strange to me. I...

10 November 2016 2,384 7 View

Hello, How may we merge the .itp files contents when we using Amber force field in gromacs?

Hello, I have generated ligand's topology files through acpype, the number of ligands are two. when we want to run simulation on gromacs, we gonna merging the two files especially their atomtype...

09 October 2016 4,798 0 View

Which is suitable for use with Python? MySQL or SQL Server?

Which is suitable for use with Python? MySQL or SQL Server? What is your suggestion?

01 March 2021 3,422 3 View

Can Virtual Servers (remote dekstop manager) run heavy ANSYS Fluent CFD simulation ?

I have a virtual machine. My host Pc specs are not that good thats why i went for virtual servers. so basically my host pc has 8gb of ram with nvidia quadro k2200 4Gb DDR5 GPU ,processor intel...

01 March 2021 8,415 1 View

What is the most suitable server for predicting protein structures in bacteria?

I have used the i-Tasser several times, however it has been unavailable for several days. I tried the swiss-model, but the output was not very pleasant due to the model used. Is there any other...

28 February 2021 4,521 3 View

Trouble with Charting with Google Earth Engine (Technical)?

Hello. I have a problem with the charting in google earth engine. I created an image collection by combining 5 image collections of five parameters and using ee.Join.inner ( ) and .apply ( )...

26 February 2021 7,084 2 View

Can the problems of overfitting be solved without cross validation?

For an overfit data set the cross validation error will be much bigger than the training error. Is it true or false?

23 February 2021 3,616 2 View

How to manage western blot for proteomics data validation?

Hi Everyone, I am a bigginer in western blotting and I am trying to use it for validation of my proteomics data. I have: two regulated proteins with molecular mass of 40 and 73 kDa one control...

23 February 2021 6,671 4 View

Best excel chart to compare algorithms' running time?

Hi I want to compare the running time of robotic path planning algorithms. The grid size is 8X8. I have 100 scenarios of start and goal positions.. Each scenario is run in three obstacles ratio...

22 February 2021 621 1 View

Alternative to mediation analysis?

I am currently working on my dissertation and want to explore the role of competence as a mediator between the effect of colour of clothes on voting intention (focus on Western countries)....

21 February 2021 8,609 1 View

Color of spiro-ometad film?

What does the color of a spiro-ometad film indicate? I got purple, green, red, even black color of the spiro film. Is there anything we can get from the preliminary color analysis(e.g. oxidation...

21 February 2021 1,831 4 View

Any information about dinitrosalisylic acid reagent end point color stability ?

I work on estimation of alpha amylase activity using dinitrosalisylic acid reagent If i put the reagent to stope the enzymatic reaction and allow the reagent to react with the produced reducing...

17 February 2021 7,402 4 View