Anything in AMBER?
Yes, you can use WHAM-2D
I am planning to calculate binding affinities for a set of ligands to my protein of interest, both the wild type as well as mutated form. The crystal structure for the particular conformation of...
08 September 2015 9,786 6 View
I have docked a known inhibitor to my protein and the initial docking energy was ~ 5Kcal/mol. I ran 40ns simulation using AMBER and when I performed MMGBSA analysis on this complex, the binding...
07 August 2015 8,933 7 View
05 June 2015 9,121 6 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 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 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
Dear all, I just saw this example in FB on the difference between laminar flow and turbulent flow. The flow from a pipe hits the sink and scattered. The flow from the pipe is characterized as...
02 March 2021 1,999 5 View
Dear All, I have access to some rodent fecal samples that have been stored at -20C instead of -80C. Anyone have experience with the impact of stowage condition on comparative metagenomic analysis...
01 March 2021 2,512 1 View