Has anyone here run BFEE NAMD on windows and had success?
- If you already did, could you describe the steps please?
- I am trying to calculate the energy of the protein-binding complex and I have not been successful.
Check these out:
https://www.www.ks.uiuc.edu/Research/vmd/plugins/bfeestimator/
BFEE (uiuc.edu)
https://drrajeshsingh.wordpress.com/tutorials/free-energy-calculations/free-energy-calculations/
Free Energy Calculation: NAMD | Molecular Modelling and Pharmacoinformatics (wordpress.com)
https://listoffreeware.com/free-energy-modeling-software-windows/
4 Best Free Energy Modeling Software For Windows (listoffreeware.com)
Mr. Riaz thanks for your feedback, it will help me a lot
Hi, I have problems with running gel electrophoresis. I have tried agarose gel electrophoresis and native PAGE. I have two proteins, which have molecular weights of ~30kDa and ~180kDa and two...
03 March 2021 4,275 4 View
Hi, im trying to make a projection in a 3d comsol model. I have a non uniforme chanel and my intention is to get the average tempreture in the y-z cross section and se the average tempreture...
02 March 2021 4,624 4 View
I am going to have a expression cloning of mammalian gene by using shuttle plasmid to transforming the E.coli However I don't know I should only inserting the Coding sequence ,or I can...
28 February 2021 5,440 3 View
Hi every body I need to collect datasets from different source to work on recommendation system algorithms, could you advise me how collect data?
27 February 2021 7,063 7 View
To be specific, I want to conduct an IV regression in stata with the following three equations. EQ1: Y1 ~Y2 Y3 X EQ2: Y2 ~ Z1 EQ3: Y3 ~ Z2 Both Y2 and Y3 are endogenous. However, Z1 and Z2 are...
23 February 2021 6,266 3 View
We have thin roots of from 1 year old different species of plants. We are looking into anatomical details of the roots. What's the best method to preserve and process the roots once they are...
23 February 2021 1,898 1 View
Hello I try to install and run the VMD software on windows 10 (64-bit).It doesn`t work and it is closed when I run it. I checked all of tutorials, videos and documents. But they did not work...
22 February 2021 8,211 3 View
I will start to fabricate micro/nanoparticles for growth factor release and I check out a procedure quite nice, however, it is lacking some details and since I don't have much knowledge doing this...
20 February 2021 199 2 View
About crack modeling in ABAQUS: Mode I (pure-tensile cracking) and Mode II (pure-shear cracking), these assumptions may be accruing in theoretical approach (ABAQUS) not practical in Lab....
19 February 2021 6,156 1 View
17 February 2021 8,533 2 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
Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...
02 March 2021 4,569 4 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