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Questions related from Sunidhi Bhatt
Hello, I am working on bacterial enzyme-mediated degradation and am particularly interested in cytochrome P450 enzymes. If you have experience with expression, functional assays, I would greatly...
last month 2,825 1 View
How to generate ligand.itp and ligand.gro files for md simulation using amber14 force field?? Kindly help!! Thanks in advance.
13 November 2023 2,477 4 View
I'm trying to generate ligand topology files through CHARMM FF but i'm getting this error. I installed the respective python version but error is still same python cgenff_charmm2gmx.py UNK...
24 October 2023 1,636 4 View
How can I insert a protein structure model within the Lipid bilayer structure model? Kindly help.
13 May 2023 5,124 3 View
what are the alternate servers for PRODRG to generate ligand topology? I have tried ATB, ACPYPE also but ligand gets detached from the protein while generation complex.gro file in the MD run....
24 April 2023 7,813 3 View
Which tools are best for prediction of binding pocket or active site of protein to perform molecular docking? Thanks!!
23 February 2023 5,880 3 View
I'm searching for free software for the QMMM calculations of protein-ligand complexes. Kindly suggest.
14 January 2023 5,922 7 View
I'm trying to calculate binding energy of md simulation trajectory by g_mmpbsa. But van der Waals forces are very high. What should i do to lower the vander waal forces?
14 December 2022 3,890 2 View
How can I calculate binding free energy between protein and ligand complex after running protein_ligand complex md simulation? Thanks in advance!
26 July 2022 9,434 2 View
I am performing protein-ligand complex MD simulation after docking. The ligand stays intact intially but is found far away in md.gro file from protein during the md run of 100ns. Kindly help me...
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