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Hi there!
I am modifying parts of this code for some specific runs and was just wondering as to the behaviour of specific parts with respect to the ligand only phases. I am just clarafying this as …
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MAOB has 4700 positive scores. Initially, I thought this must be because the box was too small, since that was the reason for the positive scores in other targets. However, that doesn't make a lot of …
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**Describe the issue**
Trying to install gmx_MMPBSA getting following error.
amber.python -m pip install gmx_MMPBSA
/home/muzzammel/amber/amber20/bin/amber.python: No module named pip
I chec…
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Your example for flexibledocking is failed.
```
(base) liuyujie714@ubuntu:~/Documents/flexible_docking/solution$ ./vina_1.2.1_linux_x86_64 --receptor 1fpu_receptor_rigid.pdbqt --flex 1fpu_receptor_…
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Over the past few years, people have slowly been figuring out how to combine small molecules with protein complexes in an efficient and understandable manner. The pipeline is always something followin…
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It would be helpful to parse the actions from BNGL files.
The `simulate` action in the example below isn't parsed.
```python
import bionetgen
model = bionetgen.bngmodel('LR_comp.bngl')
model.…
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**Describe the issue**
I performed charm36 ff based MD simulation using Gromacs 2018.1. I am able to calculate g_mmpbsa based binding energy calculations.
**_If you will report an error, please co…
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Hi, I have questions for your paper: Generating 3D Molecular Structures Conditional on a
Receptor Binding Site with Deep Generative Models.
1. You include binding pocket in both encoder and decode…
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Hello,
After updating to the most recent version I got such an issue:
Can you give…
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Hi, I am working with flexible docking, and compared to nonflexible docking it is giving very high scores: 2252099169.975 kcal/mol and is taking very long to run per protein. Could you kindly tell me …