I am calculating its MM/PBSA of protein DNA complex having magnisium ion as a part of receptor in which I got this error every time
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I want to Estimate surface heat fluxes using MyLake, but I don't have all the initial values in model parameters section and other sections,is there a way?
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why don't d-orbitals split themselves because of themselves without the presence of ligands? Electrons are indistinguishable. Why wouldn't it be more correct that protons from a ligand split the...
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I'm guessing it's because the ligand experiences too much electron repulsion or proton repulsion from the chromium to insert them close to the 3d-orbitals which are close to the metal nucleus. Is...
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Hello, I am doing ONIOM QM/MM energy calculation. I am adding explicit solvent. My input keywords is below: # oniom(m06/6-31g(d,p):amber=hardfirst) scrf=(iefpcm,read,oniompcm=x) nosymm...
04 June 2024 5,825 1 View
Hi, I'm new to QM/MM calculations, and I've recently started a calculation for a laccase enzyme containing 4 Cu ions. Following the Ambertools MCPB.py tutorial, I've created these files:...
30 May 2024 7,237 0 View
I have completed MD simulations of protein -DNA complex upto 200ns using Amber tools but when I am calculating its MM-PBSA I have the same error every time
10 February 2024 2,623 2 View
i am doing oniom calculation QM/MM for CYP450 and a drug as ligand. here i put my input file and the log file. i have been building this system for 3 weeks. this time i can't find out where the...
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[INFO ] Running calculations on normal system... [INFO ] Beginning GB calculations with /home/bio/anaconda3/envs/gmxMMPBSA/bin/sander [INFO ] calculating complex contribution......
01 January 2024 2,255 6 View
Hello, I have performed MM-PBSA calculation of a protein-ligand complex. I utilised approx 750 frames (out of a total of 15000 frames) to compute the free enrgy change of binding. Then, I used a...
04 October 2023 247 2 View
Hello everyone, I am currently facing an issue while attempting to perform MMPBSA calculations. I encounter the following error message: "ModuleNotFoundError: No module named...
21 September 2023 3,172 0 View
I have processed 100ns MD simulation studies with only protein and protein with ligand (with various analyses like- RMSD, RMSF, rGy, hbond etc) but the reviewer asks to calculate the solubility...
19 June 2023 616 1 View
source ------https://rashmikumari.github.io/g_mmpbsa/single_protein_ligand_energy_contributions.html
12 June 2023 2,253 1 View
Let us say binding free energy is -80, then + 130 kJ/mol error bar. So how far is it correct?
02 June 2023 5,471 5 View