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Hey,
This method looks really nice, and I am hoping to apply it on my system of interest. Unfortunately, I am running into an error if I try to analyse simulations of a dimer as opposed to just a …
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PyDP4.py -f mmff -w gnomesw -m t -s b3lyp --InChI Inchis.inchi experimental_nmr_files
```
Setting up Tinker files...
Tinker input for InChI_Mol_0_0 prepared.
Running Tinker...
/appl/soft/chem…
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FindPotentialStereo() fails to find centres in bridged bicyclic systems involving a 4-membered ring.
See original rdkit-discuss [here](https://sourceforge.net/p/rdkit/mailman/message/37285715/).
F…
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**Submitting author:** @wongzit (Zhe Wang)
**Repository:** https://github.com/wongzit/ICSSgen-ICSScsv
**Version:** v2.0.0
**Editor:** Pending
**Reviewer:** Pending
**Managing EiC:** Daniel S. Katz
**…
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In order to compute the contacts between the protein and ligand, I wanted to select just the heavy atoms i.e. avoiding any hydrogen atoms. I was wondering since the MDAnalysis selection criteria and t…
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Hi, @GMashayekhi
Thanks for the previous explanation. I have a question about editing file "slcPsinums.mat" which is needed in "Propagate the CC" step.
Based on my understanding, the file slcP…
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Potentially very useful. Not sure why we don't have it yet... Maybe too many? Probably make sense to activate once we have a proper UI for the filters.
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Tracking the support issue from May 21 where an author sees 98 new publications, some of which appear to be duped.
Justin Littman and I looked at the support issue this morning for a couple hours, an…
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With classical MD for a protein and its peptide ligand I am observing repeating sudden raising of RMSD vs frame followed by flat regions, typical of conformational changes. As a novice to ProDy, I wou…
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Wonderful work! This package will helps us a lot!
I have an issue when I was using this package analyzing the Demo-data, Ryr1, in the tutorial.
In first several steps I got good results, the …