I am trying coarse grained molecular dynamics in Windows systems for some peptides. I need a program for this purpose. Can anybody suggest me?
I want to use a pdb file got after docking of a ligand to protein using autodock4 in molecular dynamics calculations with the help of VMD and NAMD only. I have a very little idea about VMD as well...
08 September 2018 7,947 0 View
I was tried the keyword "polar" for the calculation. I was unable to get the result. I need a suggestion about it. Please tell me keywords that I can use it in Gauss view 5.0 for calculation....
07 August 2015 1,468 7 View
I can not make flexible and rigid.pdbqt files of DNA. I can not select sugar and nucleotides separately .
31 December 2014 8,009 4 View
When I want to upload structure factor file after uploading cif file in Acta ctystallography sce E they show 'Our records show that you have already uploaded an article with this title.' Please...
09 October 2014 7,654 0 View
Method to get supplimentary data using Appex and WinGX software or any other sources?
31 December 2013 8,393 3 View
I have no idea about compiler. Please help me.
01 January 1970 4,995 0 View
"PUBLISHING IN A SCOPUS JOURNAL" Researchers are now at a cross road. The critical need to publish in a Scopus or ISI, etc journal is ever vital. Journal Publication fees must be submitted....
10 August 2024 8,621 1 View
Hello experts, Does anyone know any free software about retention index prediction ?
08 August 2024 7,403 2 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
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
I have an antibody binding generic protein and I need to compare its activity in a free and immobolized form. I understand that there are a number of methods to determine Kd value of a free...
05 August 2024 5,311 0 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