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I went back and had a look at the [NGL viewer](https://opensourceantibiotics.github.io/murligase/ngl/examples/MurDwebapp.html?script=interactive/MurD_ligand-viewer) of Fragment 373 for MurD (#1) and n…
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Hi,
I've been running MD simulations using OpenMM and want to carry out water analysis using GIST.
While I haven't restrained the protein using strong position restraints, as suggested by the [tu…
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Hi,
I'm using GIST to measure energetics of water displacement upon ligand binding to a protein cavity. I've been following this [tutorial from ambermd.org](https://ambermd.org/tutorials/advanced/tu…
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Hi,
I am using `PyAutoFEP` to calculate the free energy values of 3 pairs. Previously, my other simulations were conducted by `amber14ff` via `gromacs-2022` and I would like to use them here as we…
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[Greenidge, Paulette A, Christian Kramer, Jean-Christophe Mozziconacci, and Romain M Wolf. “MM/GBSA Binding Energy Prediction on the PDBbind Data Set: Successes, Failures, and Directions for Further I…
cramg updated
3 years ago
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Dear Dr. Qifeng Bai,
I work in computational chemistry. I have been using the MOLAICAL code for MMGBSA calculations for NAMD 100ns trajectories, and it has been working greatly, specially with the ne…
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I am trying to run yank on a system where the ligand is a peptide, and it does not seem to recognize the peptide for alchemical modification, such that all of the "alchemical" states are exactly the s…
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Hello,
I would like to run a simulation of a ligand binding to a protein with a co-factor. I see in an earlier post (December 14-16) it was stated that one could run with a co-factor by including i…
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Hello,
I have a question regarding the calculation of transitions between ligands with different total charges.
As per the tutorial, I've followed the steps to prepare equilibrium simulation fil…
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Hi 👋! In the paper it is mentioned: "For DIPS, the split is based on protein family to separate similar proteins". Is there a source code for this split? I could only find a [random split in `parititi…