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Questions related from Jonathan Purnomo
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:...
31 May 2024 7,201 0 View
I have a research using MD simulation (using GROMACS) for proofing the binding stability of protein-protein interaction. To measure whether the interaction is stable, I wish to employ binding...
05 March 2024 4,088 1 View
Hello, I'm currently trying to determine the degradation product of malachite green using GC-MS. I have the raw .D file and needed a library for the interpretation of MS spectra. I have tried...
29 November 2022 9,871 0 View
I read a paper on malachite green separation using TLC method that, i assume was, describing pretreatment of silica gel with chloroform. The exact word used was "Metabolite formation was examined...
08 July 2022 8,764 3 View
I have a molecule that i want to simulate using gromacs. As i tried pdb2gmx, there is no error in the console, but the topol file did not record any [moleculetype] datas. It did not hinder the MD...
31 December 2021 5,651 3 View
I want to analyze the interaction of an enzyme with small molecule of an FMN (flavin mononucleotide) but gromacs doesn't recognize FMN. It require for manual definition of FMN topology. Using...
24 September 2021 8,926 3 View
I've seen in some articles talked about parameterizing ions force field, for example here Effect of Ca2+ on the promiscuous target-protein binding of calmodulin the authors talked about...
05 August 2021 6,948 1 View
