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I am currently using your code to build models with hydride ligands. I noticed that the 'relax' parameter is set to 'False' when hydrides are detected as SMILES (in io_process_input.py, lines 427 and …
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Prepare and process data related to "isolated ligands" thread of JT-VAE modelling.
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Hi Chai team,
I encountered an issue when predicting protein-ligand structures using the Chai-1 web server. It appears that all ligands in the predicted structures are renamed to “LIG”, which preve…
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Hello,
I think hydride has great potential for its versatility and speed. I have tried many tools for adding hydrogens from structures over the last months, but hydride is the best for me, togethe…
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Hello everyone, I'm currently using Vina for docking multiple ligands and have a question about the output. Does the binding free energy reported by Vina take into account the interaction energy betwe…
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Hello,
i'm working with Helixfold3 for virtual screening between a protein and a list of ligands. For some ligands, i've the error:
File "/softwares/helixfold/3/PaddleHelix/apps/protein_folding/heli…
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I created unpaired and paired MSAs using jackhmmer searches and created two separate MSA contexts out of them. However, when you combine protein complex modeling with a ligand, the AllAtomStructureCon…
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Hi! It's me again :)
To simulate cofactors one can use the [manchester university database](http://amber.manchester.ac.uk/) of parameter modifications. For example to simulate PDB 2FDV, one can ext…
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Parameterizing the entire peptide ligand with OpenFF takes far too long.
The next workaround to try is to parameterize only the nonstandard Amino Acid with Openff, and the rest with AMBERFF14SB
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Thank you for developing chai-lab, which is an amazing tool and has greatly assisted my work. However, when I try to input the trivalent iron ion in the ligand part locally using chai_lab with the com…