I am using Gromacs to simulate a peptide (force field: Gromos96 54A7 and coloumb type= PME).
And can we use it for conversion of any of the peptide (in Beta form) to its monomer form?
11 December 2015 7,434 4 View
We intend to study the interaction between peptides and polymer (like PP, PE and PS) through MD simulations using Martini force fields ( Martini 2 for PP and Martini 3 for PE, PS). We have...
08 August 2024 4,842 0 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
Hi, we have measured tryptic peptides using both DDA and DIA method on QExactive. In DDA replicates i saw unusual intensity drops occurring at the same sections of chromatograms in DDA replicates...
07 August 2024 3,218 4 View
Hi, I know that low molecular weight (MW) molecules generally tend to have higher mobility, while high molecular weight molecules tend to have lower mobility. However, in my experimental...
06 August 2024 1,495 2 View
kindly reply me. Thanking you in advance.
05 August 2024 7,727 4 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
Is it possible to conduct a molecular dynamics simulation to see the effects of a specific carbohydrate on the structure of lipids (e.g., micelle structure)? I am a beginner in this field and plan...
03 August 2024 3,371 3 View
I am using a windows system, what software I should use for hydration shell analysis with molecular dynamics?
02 August 2024 3,143 4 View
Molecular docking software/ websites?
02 August 2024 8,704 7 View
Recently I'm trying to use Sep-pack C18 1 cc Vac Cartridge (Waters: SKU: WAT054955) to desalt digested peptides. However, the recovery rate is usually 40-60%. What is the normal recovery rate?
31 July 2024 6,544 11 View