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I want to understand the how the thermodynamics and kinetics has changed due to ligand binding. So we have performed several short (1 microsecond) MD simulation with and without ligand.
We are using…
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Funnel meta-dynamics, is meta-dynamics where we restrain ligand in a cone/cylinder-shaped potential, where the ligand expriences potential K, when outside cone/cylinder and no potential when inside. I…
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Thank you very much for providing such a great molecular generation model.
May I ask, does your model support protein receptors containing metal ions at binding site? I have attempted to use these …
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When running Uni-Mol Docking V2 via the demo.sh script on a custom protein-ligand, every part of the process seems to complete successfully, but the result file for the ligand is different than the in…
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The (soon-to-be-implemented) treatment for this is:
* We do not add the restraint to the fully interacting state if in explicit solvent.
* We add the restraint if in implicit solvent/vacuum.
Is t…
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Hi, I want to do covalent docking using autodock gpu with ligand prepared by `mk_prepare_ligand.py`.
However, I need help.
1) I followed the instruction below.
https://github.com/ccsb-scripps/A…
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interacting_pair is ligand_receptor or receptor_ligand?
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Hi pdb2pqr user!
I have complex structure of receptor and ligand in the pdb format. I am trying to convert this pdb file into pqr file format for binding energy calculation. During running command li…
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I downloaded the BFEE VMD plugin and was looking to perform binding calculations for a protein-protein system. I noticed that it does not let me select the protein:protein option and only allows for t…
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**Describe the bug**
I've recently been trying to implement multiple distance restraints for absolute binding free energy calculations in BioSimSpace and SOMD ([modified BSS](https://github.com/fjcla…