When I solvate the protein in AMBER16. EPW H2O shown in (AMBER output file) solvated PDB file.I don't understand what is the meaning of EPW. I have attached screenshot. kindly let me know.
I have run the required calculation for the force constant value in Gaussian successfully and have converted the file.chk file into fchk via formchk. So is there any software which can give...
03 April 2018 924 0 View
I want to know how calculate the resp charge. I have followed the tutorial for understanding of resp charges in amber 16. For calculating the charge i have used only "linker part"...
10 November 2017 4,276 1 View
I am facing a problem in (0GA+ROH) GLYCAM carbohydrate parameter while doing force field preparation for glucose molecule in AMBER. I have used Gaussian optimized structure and calculated the MK...
10 November 2017 3,158 0 View
I have two different set of graph one set is starting from 0-200 and one set is 0-200 on x-axis. how can i merge both sets in xmgrace so that the total graph should be 0-400. means the x axis has...
10 November 2017 1,873 1 View
I have serine aa in the core of protein behaving as a positive entity which i inferred from electropotential surface. as it contain OH negative its should behave as negative entity. I am not able...
09 October 2017 8,485 1 View
I have try to simulate a protein with Ag+ ion with ff14SB at AMBER16. When I type in tleap script they showing message vdw parameter is not find. how can I set a parameter for Ag+ ions. please...
31 December 2016 7,743 4 View
Approximate concentrations are require in compared with the WHO permissible limts
11 August 2024 2,723 1 View
I am developing a predictive model for a water supply network that involves 20 influencing points. However, I only have historical data for 10 out of these 20 points. I would like to know how to...
10 August 2024 4,005 2 View
How do interactions between the biosphere, the carbon cycle, and the water cycle impact global warming and interaction between the atmosphere and the hydrosphere?
09 August 2024 3,291 2 View
One can try to generalize the Vandermonde determinant in the following direction: Let $A$ be any symmetric $n$-order square matrix. Consider its powers' diagonal elements $(A^k)_{ii}$ and...
08 August 2024 6,690 1 View
I'm working on selecting antibodies against a recombinant protein that has a His-tag. My idea is to first bind the recombinant protein to a HisTRAP column and then use this column for an affinity...
07 August 2024 505 3 View
I have protein-membrane simulations (PDB, PSF, DCD) and have noticed that water molecules near the protein are not visible in the simulations. How can I fix this issue? Is there a way to place the...
04 August 2024 1,200 2 View
Why is nonpoint source pollution potentially more harmful and difference between point and nonpoint sources of water pollution?
01 August 2024 1,180 2 View
How do living organisms play a role in the water cycle and why is nonpoint source pollution potentially more harmful than point source pollution?
01 August 2024 7,061 2 View
Is it the "elution buffer" or the "dialysis buffer"? Note: I'll be using NanoDrop OneC
01 August 2024 967 3 View
Hi, I'm curious to know if data on chemical compounds from PubChem, such as water solubility properties, can be used to train a machine learning model for commercial purposes. Will this infringe...
30 July 2024 8,707 1 View