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Hello,
I have been starting to work with nitrogenous surface species and have been seeing something odd and unintentional happening. It seems that RMG is applying reaction templates that do not fit…
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**What are you trying to do?**
I am considering the predict the property of molecule in the solvent, so two molecules should be input into the gnn at the same time.
While i have additionally calcula…
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**Github username:** @Al-Qa-qa
**Twitter username:** al_qa_qa
**Submission hash (on-chain):** 0x590efc11e1735caefc941a4b813422392ade726f0329ac1117feaa01cc1b8388
**Severity:** low
**Description:**
**…
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I cannot get refinement to work when the residue ID is larger than 9999 for one of the linked atoms. For example, with PDB 7K00, the link between MG and HOH in chain 'a' causes this error.
Command:…
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Hello,
mdtraj's image_molecules was failing for some of our systems, and I could trace the source of the bug to `make_whole` in [image_molecules.pxi](https://github.com/mdtraj/mdtraj/blob/fd80ab1c1…
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Hello, I was ready to run your model in lammps today, but I was told that the atomic format does not meet the lammps specification because of the lack of molecle-tag. In addition, I would like to ask …
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# What happened
I remember that when we discussed the concept `ONE` in prehistoric times, we decided not to have a syntax for its atom. The idea was that we thought we didn't need it. So we decided t…
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How to delete one of the atoms and the corresponding key after loading a pdb file ?
Thank you for your help. Best Regards
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### Setup
I am reporting a problem with Biopython version, Python version, and operating
system as follows:
```
3.10.0 (default, Nov 10 2021, 13:28:23) [Clang 12.0.0 ]
CPython
macOS-14.0-arm…
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I am trying to get the thickness of a simulation of a DOPC membrane over time. I first made an index file with all the phosphates and lipid tails selected (groups 'PA' and 'OL') and then used that as…