I need to deprotonate a specific cysteine. How to do this for charmm in the Gromacs 2020? Is it necessary to modify the force field or just a simple deprotonation?
an introduction
02 June 2024 520 0 View
I will be grateful if i can get the latest work on the above topic.
17 May 2024 2,509 1 View
I'm challenging bacteria with different compounds, then plating the suspension on LB agar to assess CFU and understand the bactericidal properties of my compounds. However, I'm encountering...
10 April 2024 7,459 7 View
I am using the Thermo Scientific DNase I (https://www.thermofisher.com/order/catalog/product/EN0521) to remove genomic DNA from RNA extracts eluted in nuclease free water. The protocol calls for...
30 March 2024 7,100 0 View
My watershed keeps showing there's no overlap with the watershed grid and I have clearly projected it in the same projection as the watershed and source dem. WGS 84, UTM 32. But when try to use...
18 February 2024 1,304 1 View
Animal collected in Brazil, southern region, associated with the sea urchin Echinometra lucunter. Only one animal was found.
28 January 2024 9,206 4 View
i would like to ask, wheather autocorrelation desciptors are sub type of 2d or 3d desciptors , they are offered by many platforms to calculate without demon about the differnce between them and...
09 December 2023 8,714 3 View
There's a great app called ChemSketch but only compatible with Windows. I'm looking for similar options for a Mac user. Thnks!
29 November 2023 3,237 2 View
I did an experiment where I evaluated the growth of colonies of a bacteria in different samples. For one of them it was not necessary to do serial dilutions. In this case my dilution factor cannot...
19 November 2023 3,608 8 View
hallo everybody , iam using autodock vina for small molecule docking , however after finalizing everything with the grid the running of autogrid cannot be predeeded and no gld file is created with...
04 November 2023 5,952 2 View
I have face this problem anyone help me how to solve this issue ?which is below Fatal error: There are inconsistent shifts over periodic boundaries in a molecule type consisting of 78 atoms. The...
07 August 2024 2,598 1 View
Hello, I am currently analyzing some phosphoproteomics data, but I have peptides with multiple phosphorylation sites or phosphorylations together with carbamidomethylation or oxidation. How can I...
04 August 2024 8,432 3 View
When we conduct linear regression, there are several assumptions. The assumption of normality is whether the residual errors are normally distributed, not whether a predictor is normal?
31 July 2024 6,164 3 View
Dear All Gromacs User I would like to restart MD without using checkpint .cpt files? I heard there is a way for acheiveing this. Any input and sugegstions are most welcome. Thanking You Budheswar
29 July 2024 3,084 8 View
I wanted to know whether we can observe the synergistic/antagonistic/additive properties of combinations or mixtures of compounds through docking analysis. But during docking preparation any...
28 July 2024 7,413 6 View
If I want to calculate molecular dynamics (Gromacs), do I first need to optimize the geometry of the molecule? For example, I first draw the molecule in Avogadro, and then what? I guess I can't...
28 July 2024 673 3 View
Dear users, I would like to simulate a zeolite structure in gromacs. I got the .cif file from IZA expanded in one direction in Materials Studio and exported a .pdb file. However, when I want to...
24 July 2024 367 4 View
Kao's panel cointegration tests , is there anyone willing to explain me the eviews-9 output for the Kao's panel cointegration tests?
23 July 2024 5,051 4 View
Methionine, cysteine, homocysteine, and taurine are the 4 common sulfur-containing amino acids, but only the first 2 are incorporated into proteins. Sulfur belongs to the same group in the...
22 July 2024 4,273 4 View
I want to express STK4, and I've searched the paper for reference. When I check the protein kinase domain sequence for that kinase on Uniprot, it's 30-281, but the paper expresses the protein...
20 July 2024 4,951 1 View