I have one transcription factor, so how do i have to do dock with DNA? how can i create PDB file of DNA? what is the procedure for simulation in gromacs? can you suggest anyone?
RNA structure prediction
01 February 2018 3,909 0 View
why only these denaturants used why not others can anybody give explanation for this?
01 February 2017 6,569 0 View
I have done molecular docking of one protein and ligand but i don't know how do i have to calculate free energy in between these two molecules? can you suggest anyone commands related to this?
11 December 2016 2,140 1 View
i am getting big crystals by increasing MPD from 40% to 60%, is the possibility of getting mpd crystals or they are protein crystals, those crystals are not well formed plz give suggestions.
11 December 2016 6,837 1 View
Please can any one suggest me preparation or how to dissolve gingkotoxin for my experiments?
09 October 2016 4,771 4 View
i have protein dimer sequences of chain A and B, how can i model these two sequences? i want to get as dimer. is there any software ? can you suggest?
09 October 2016 7,064 1 View
How do we have to incorporate metal in model structure of protein? is there any option in autodock? i want to do docking small ligand along with metal?
09 October 2016 9,319 1 View
08 September 2016 9,709 3 View
Basically how many nanoseconds we have to use for protein simulation? i used 20 ns for modeled structure, is it sufficient or shall i increase the time? can you suggest anyone?
08 September 2016 5,569 8 View
How to calculate the RMSD values for a MD simulation using MOE?
07 August 2021 0 0 View
When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.
16 June 2021 0 0 View
Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...
03 March 2021 9,989 2 View
Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...
03 March 2021 5,978 5 View
Hello, I'm fairly new to ARENA and I have the following problem: I have two queues in which, in each queue, a different order type arrives (both having an arrival rate of exponential 10). Order...
02 March 2021 2,431 3 View
Hello, I have a mechanism where air rises due to convective flows. In this simulation, nothing is driving the air except this. I understand that the Boussinesq approximation only works for small...
02 March 2021 4,910 3 View