I optimized my structure and calculated the frequency of that. I used Gauss view but need a command or instruction to calculate the exact force constant for my interested bonds.
Hello every body I want to calculate the center of mas for a protein. I want to know which amino acid the center of mass hold on. pleas give me a full help. thanks
31 December 2017 533 8 View
Hello every body I want to calculate the pattern of salt bridges and hydrogen bonds between two specific part of the protein througut the for the 10 last ns of a gromacs simulation trajectory....
31 December 2017 349 3 View
Hi every body I work on Wnt/beta catenin signaling pathway. I have a drug which is effective on non metastatic SW480 cell line. I want to test it on metastatic cell line SW620. the pathway is...
11 December 2017 1,765 4 View
Hello every body I want to calculate the antrophy amount of a protein-protein complex using gmmpbsa module of gromacs. I can calculate binding energy but not antrophy. If you have any...
11 December 2017 8,780 1 View
hello I have a protein with a calcium ion. I edited the PDB file, renaming the calcium to CA, as atom name and atom type and pdb2gmx, runs successfully. but know I worry becuse some viewers...
01 February 2017 6,827 0 View
I want to express a 37 a.a, 43 a.a and 55 a.a peptides using pET His6 Sumo TEV expression vector with BioBrick polypromoter restriction sites (14-S). the vector host is XL1 blue and the company...
08 September 2016 5,339 3 View
I need to know the position of two helices in a structure in comparison to each other. so I should to calculate the variation of their dihedral angles versus time. there is an article in the...
05 June 2016 9,864 2 View
hello I have 200 ns simulation of a peptide and i want to calculate average structure of the simulation. I used this command: g_rmsf -f md.xtc -o rmsf.xvg -s md.tpr -ox av.pdb The resulting pdb...
05 June 2016 481 4 View
I have a hard exam in x-ray crystallography. i need your help to pass it. i need a reference to understand phase problem solving. any help is appreciated.
04 May 2016 3,366 1 View
Hi is there any instruction to refold Denileukin diftitox(ontak)? it is really vital for my project. every help is appreciate.
09 October 2015 5,040 0 View
Hello experts, Does anyone know any free software about retention index prediction ?
08 August 2024 7,403 2 View
I'm currently working on calculating the collision cross section (CCS) for various ions, and I'm facing challenges when dealing with sodiated and multiply charged ions. Most of the resources I’ve...
08 August 2024 8,329 0 View
After immunohistochemistry of previously fixed in PFA and EtOH and then frozen 20 μm sections of zebrafish brain, DAPI staining is very weak (right) compared to the same sections stained without...
05 August 2024 9,637 2 View
Brain and body mass together are positively correlated with lifespan (Hofman 1993). The duration of neural development is one of the best predictors of brain size, and conception is the best...
05 August 2024 6,247 3 View
I am interested to know the behavior of dyes toward light. Specifically, Blue dyes re-emit the spectrum, especially from the green zone (known as principal in LED lamps, and blue dyes are known...
05 August 2024 3,290 1 View
Hello, everyone. I have tried to determine carrier motilities of some materials, by Density Functional Theory, using Quantum ESPRESSO. There are a few methods to do it, like a package called...
04 August 2024 8,894 1 View
Molecular docking software/ websites?
02 August 2024 8,704 7 View
I'm trying to perform a frequency calculation using Gaussian via MOBAXterm. The output shows no errors, however, there's no frequency as a result on gausview. The option "vibrations" is not...
31 July 2024 631 4 View
I am currently working on a project involving liposomes and need to determine the maximum volume of siRNA that can be added to a 2.5 mL liposome solution with a total lipid concentration of 10...
30 July 2024 6,420 1 View
Dear all, I am working on particle deposition in human's & rat's respiratory airways using CFD and I am looking for the 3D CAD file for my simulations (STEP or IGES format). If somone has such...
29 July 2024 1,092 2 View