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Hello,
Thank you so much for this public available repo.
I want to train or test these models on my structures. However, there is no script for generating the input files (i.e., the protein,…
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Hi,
I am trying to review this tool for my channel at https://www.youtube.com/@fahdmirza and facing multiple errors. Could we please connect as I am in middle of creating video and would appreciate…
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Hi,
I have had it in the past too, that when I use ``strucio.save_structure`` to save the frame from a loaded
MD trajectory, e.g. an XTC or in this case DCD file, that the resulting structure was…
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I run this code for proteins solvated in hexane. But some of my structures look like this and are just dispersed in space. no bonds.
my code:
```
from openmm.app import *
from openmm import *
…
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### **Description** Transferred from https://github.com/sars-cov-2-variants/lineage-proposals/issues/1594
**Sub-lineage of:** KP.2.3 (= JN.1 + S:∆S31, S:H146Q, S:R346T, F456L, V1104L + ORF3a:K67N + O…
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### Bug summary
Now there is a topology file with 6719 atoms, but gmxMMPBSA recognizes only 6718 (the 6687 atom is skipped), so that the index value cannot correspond to the topology file one by one,…
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```typescript
export function dynamicSuperimpose(ctx: PluginContext,pivot_auth_asym_id: string ) {
return ctx.dataTransaction(async () => {
const pivot = MS.struct.filter.first([
…
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![image](https://github.com/m3g/packmol/assets/128614019/efa2baa4-aea4-45ba-a95f-95240a1c5c8d)
![image](https://github.com/m3g/packmol/assets/128614019/c4d196be-2b68-45a7-8fe6-75df1bfbbb36)
Seem…
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Dear Sir,
Thank you for open-sourcing this work. After reviewing your preprint article and code, I have some questions and am wondering if you could provide some clarification?
1. I am interested …
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I successfully installed and tested all eg files and ran my own files to get protein-small molecule complex.
Although I got the output protein structure in complex with small molecule, there are some…