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Wouldn't it be possible for a non-ring fragment to have improper torsions due to non-ring sp2 atoms, whether represented as harmonic impropers or improper dihedrals? If so, the code very much looks l…
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### Description
I'm using freud Steinhardt to calculate the disorder parameter as defined by Kawasaki and Onuki (2011) https://doi.org/10.1063/1.3656762. A direct implementation in freud would be nic…
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I am using LigParGen Server for generating OPLS-AA Force Field parameters for small organic molecules. I have doubt regarding dihedral parameters. I am taking parameters from .key file. Energy express…
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Hey guys,
Hoping everyone's fine!
Maybe I'm asking a dumb question but I'm struggling with the explicit calculation of the energy derivatives and how OpenMM internally calculate it. For example, …
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Hi there,
Would it be possible for you to train a d8 ResNet18 network for me.
I'd really like to be able to have the same number of rotations as the C8 network, but within the dihedral group.
I dou…
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Hello Selim,
I hope you had nice new year holidays!
I'm writing to report a possible bug, which I suspect it's preventing me from completing a parametrization for an agarose dimer. I have gener…
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### Setup
I am reporting a problem with Biopython version, Python version, and operating
system as follows:
3.6.7 (v3.6.7:6ec5cf24b7, Oct 20 2018, 13:35:33) [MSC v.1900 64 bit (AMD64)]
CPython…
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I am trying to use grommp to write a tpr file but keep encountering the following error when trying to use amber14sb_OL15.ff:
ERROR 9 [file topol_Protein_chain_C.itp, line 142001]:
No default Imp…
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ghost updated
1 month ago