Hello! So i was doing a molecular dynamics simulation between HIV reverse transcriptase (PDB ID: 3LAN) chain A as receptor and a compound called Erisubin F as the ligand
I used a complex i get after doing molecular docking simulation between the two and then i separate them using grep command in gromacs
I already did all the steps (creating topologies, merging topologies of receptor and ligand, ionization, energy minimization, equlibration of temperature and pressure, and production). After production i visualized my simulation result using VMD Chimera, but in the complex the ligand is not present. Can anyone help me determine what is wrong? Thank you
Saad Amin Hello, thank you so much for your answer. So i did identify what's wrong. So i did a 100 ns production steps and when i used VMD Chimera to visualize the protein and ligand movement, it shows that in the 100 ns, they're still attached. However my production run until 1 ps after the set step (100 ns) and in that extra 1 ps, the ligand and protein separated. Could you help me prevent my production for doing extra step? (this happens everytime i did an MD simulation) Thank you so much.
Saad Amin sure, thank you so much! My email is [email protected]
Thank you so much in advance!
Your ligand might be missing due to incorrect topology merging, ligand parameter issues, or PBC artifacts. Ensure:
All of which can we easily done at mdsim360.com, a new platform that lets you run MD simulations entirely online without local installation.
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