auto_martini

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Unstable simulation

4

Hi, I'm trying to parametrize a small molecule. I was able to create both, the .itp and .gro files without issues. After this I first minimize in vaccum the molecule...

krlitros87

Can't kekulize mol due to what appears to be a Boost Error

3

Hi, I was trying to coarse-grain a small drug molecule tenofovir with SMILES "CC(CN1C=NC2=C1N=CN=C2N)OCP(=O)(O)O" For some reason it does not work and returns the following message: [16:13:49] Can't kekulize mol....

shushanhe3

LINCS warning

3

Hi I used your script to get parameters for some small molecules. But when i run these simulations on gromacs I get lot of LINCS warning for these simulations for...

cherpradyumnsharma

Problem of “Aborted (core dumped) ”

5

I use the auto_martini-refactor.zip on ubuntu 14.04. All dependencies are installed. I use beautifulsoup4, so I add "from bs4" before import BeautifulSoup in auto_martini.py But when I use ./auto_martini.py --smi...

diaobk

Problems with nitriles

2

Having trouble parameterising some molecules with a nitrile group. With a simple benzonitrile: `auto_martini --smi "c1ccc(cc1)C#N" --mol bni` I get the following error message ``` Traceback (most recent call last):...

SGenheden

outdated rdkit?

1

Hi, I've just installed automartini with all its dependencies. However, the following error is reported: $ ./auto_martini --smi "N1=C(N)NN=C1N" --mol GUA Traceback (most recent call last): File "./auto_martini", line 1181,...

fmqeisfeld

Problems with installation

1

Hi all, Thanks for your nice code. I want to make an observation. While installing automartini in a mamba environment, I noticed the package `charset_normalizer` is required. Then, if you...

LIVazquezS

Bumps [actions/download-artifact](https://github.com/actions/download-artifact) from 2 to 4.1.7. Release notes Sourced from actions/download-artifact's releases. v4.1.7 What's Changed Update @​actions/artifact dependency by @​bethanyj28 in actions/download-artifact#325 Full Changelog: https://github.com/actions/download-artifact/compare/v4.1.6...v4.1.7 v4.1.6 What's Changed updating @actions/artifact...

dependabot[bot]

ALOGPS can't predict fragment

2

Hi, I was trying to get the itp file for this molecule: `CCCCCCCCCC[N+](C)(C)C` I run this command: `python -m auto_martini --smi "CCCCCCCCCC[N+](C)(C)C" --mol DTAM --top DTAM.itp` and get this error:...

hliu56

Some GH steps need to run the latest version for CI to work.

anabiman