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Questions related from Sunidhi Bhatt
How to generate ligand.itp and ligand.gro files for md simulation using amber14 force field?? Kindly help!! Thanks in advance.
13 November 2023 2,406 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 1,560 4 View
How can I insert a protein structure model within the Lipid bilayer structure model? Kindly help.
13 May 2023 5,057 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 7,745 3 View
Which tools are best for prediction of binding pocket or active site of protein to perform molecular docking? Thanks!!
23 February 2023 5,843 3 View
I'm searching for free software for the QMMM calculations of protein-ligand complexes. Kindly suggest.
14 January 2023 5,864 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 3,845 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 9,384 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...
22 June 2022 1,291 2 View
