alanwilter/acpype issues and pull requests

#131 - Bump virtualenv from 20.24.6 to 20.26.6

Pull Request - State: closed - Opened by dependabot[bot] 9 days ago
Labels: dependencies

#130 - Bump jinja2 from 3.1.4 to 3.1.5

Pull Request - State: closed - Opened by dependabot[bot] 14 days ago
Labels: dependencies

#129 - abcg2 partial charges calculation method in acpype

Issue - State: open - Opened by yel21 16 days ago - 1 comment

#128 - Make ACPYPE able to handle non-ascii headers in PDB files

Issue - State: open - Opened by alanwilter about 2 months ago - 1 comment

#127 - ligand conversion

Issue - State: closed - Opened by nzlmrt about 2 months ago - 8 comments

#126 - link to openbabel in read me its not working use http://openbabel.org/

Issue - State: closed - Opened by pippo1990 4 months ago - 2 comments

#125 - Bump cryptography from 42.0.4 to 43.0.1

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago
Labels: dependencies

#124 - Amber off/frcmod non standard residue to CHARMM RST file

Issue - State: closed - Opened by pguillem 5 months ago - 1 comment

#123 - Bump setuptools from 68.2.2 to 70.0.0

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago
Labels: dependencies

#122 - Bump zipp from 3.17.0 to 3.19.1

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies

#121 - Bump certifi from 2023.7.22 to 2024.7.4

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies

#120 - Bump urllib3 from 2.1.0 to 2.2.2

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies

#119 - Bump requests from 2.31.0 to 2.32.0

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#118 - Bump jinja2 from 3.1.3 to 3.1.4

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago
Labels: dependencies

#117 - Bump tqdm from 4.66.1 to 4.66.3

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago
Labels: dependencies

#116 - Bump idna from 3.4 to 3.7

Pull Request - State: closed - Opened by dependabot[bot] 10 months ago
Labels: dependencies

#115 - more water models from Amber

Issue - State: closed - Opened by thepineapplepirate 10 months ago - 2 comments

#114 - Re-running ACPYPE with same molecule with different formal charges doesn't update the GMX itp

Issue - State: closed - Opened by serge-andre2 11 months ago - 1 comment

#113 - Bump cryptography from 42.0.2 to 42.0.4

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago
Labels: dependencies

#112 - Bump cryptography from 41.0.5 to 42.0.2

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago
Labels: dependencies

#111 - Bump cryptography from 41.0.5 to 42.0.0

Pull Request - State: closed - Opened by dependabot[bot] 12 months ago - 1 comment
Labels: dependencies

#110 - No Charge value given and wrong assigned bond types

Issue - State: closed - Opened by EsToHi 12 months ago - 1 comment

#109 - Bump jinja2 from 3.1.2 to 3.1.3

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

#108 - Bump cryptography from 41.0.5 to 41.0.6

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 1 comment
Labels: dependencies

#107 - Added Ruff to replace all other linters

Pull Request - State: closed - Opened by alanwilter about 1 year ago - 2 comments

#106 - Bump urllib3 from 2.0.3 to 2.0.7

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#105 - Bump urllib3 from 2.0.3 to 2.0.6

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#104 - Error while generating topologies

Issue - State: closed - Opened by 91Abdullah over 1 year ago - 3 comments

#103 - Bump cryptography from 41.0.1 to 41.0.4

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#102 - Handle the competition for parmGaffffxxSBFile when running acpype concurrently.

Pull Request - State: closed - Opened by 9527567 over 1 year ago

#101 - Conda installs "full" ambertools, no writing of CHARMM ff files

Issue - State: closed - Opened by jacksoncrowley over 1 year ago - 2 comments

#100 - How much time is expected to complete an instalation using conda?

Issue - State: closed - Opened by ivopr over 1 year ago - 7 comments

#99 - fix: UnboundLocalError on output variable on acs_api

Pull Request - State: closed - Opened by ivopr over 1 year ago

#98 - conversion of Amber files to gromacs

Issue - State: closed - Opened by Pz-Maajid over 1 year ago - 3 comments

#97 - Bump cryptography from 39.0.1 to 41.0.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#96 - [question] what are the partial charges being used?

Issue - State: closed - Opened by UnixJunkie over 1 year ago - 1 comment

#95 - [question] does it automatically protonates molecules for a given pH?

Issue - State: closed - Opened by UnixJunkie over 1 year ago - 1 comment

#94 - A question about the content of md.mdp file

Issue - State: closed - Opened by darekb94 over 1 year ago - 1 comment

#93 - Bump requests from 2.28.1 to 2.31.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#92 - Is the GMX_OPLS still experimental?

Issue - State: closed - Opened by BJWiley233 almost 2 years ago - 3 comments

#91 - Is there a way to control the threads?

Issue - State: closed - Opened by Dead-fisher almost 2 years ago - 3 comments

#90 - Bump cryptography from 39.0.0 to 39.0.1

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#89 - atom type does not exist in parmchk.dat

Issue - State: closed - Opened by suneelbvs about 2 years ago - 3 comments

#88 - is this a bug?

Issue - State: closed - Opened by wenyan4work about 2 years ago - 3 comments

#87 - Bump certifi from 2021.10.8 to 2022.12.7

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago
Labels: dependencies

#86 - Fix GitHub language detection

Pull Request - State: closed - Opened by boneta about 2 years ago

#85 - '1-4 pairs were missing' warning when parsing the converted topology with ParmED

Issue - State: closed - Opened by meneshail about 2 years ago - 4 comments

#84 - charmm input format

Issue - State: closed - Opened by kaiwanxiao1996 over 2 years ago - 1 comment

#83 - acpype error

Issue - State: closed - Opened by sjdyz over 2 years ago - 1 comment

#82 - Planarity of the benzene ring not maintained in dynamics.

Issue - State: closed - Opened by mayank-kohli over 2 years ago - 8 comments

#81 - changing the place where the amber environments are called.

Pull Request - State: closed - Opened by lkagami over 2 years ago - 2 comments

#80 - wrong converted charge

Issue - State: closed - Opened by qinghualiao over 2 years ago - 3 comments

#79 - multiple chain protein

Issue - State: closed - Opened by Christinele14 almost 3 years ago - 3 comments

#78 - Unable to achieve self consistency to the tolerances specified

Issue - State: closed - Opened by azbven almost 3 years ago - 1 comment

#77 - Setting basename miss several result files.

Issue - State: closed - Opened by Benstime almost 3 years ago - 2 comments

#76 - ModuleNotFoundError: No module named 'openbabel'

Issue - State: closed - Opened by purnawanpp almost 3 years ago - 2 comments

#75 - ERROR: ACPYPE FAILED: No module named 'openbabel'

Issue - State: closed - Opened by archana433 almost 3 years ago - 4 comments

#74 - FileNotFoundError: [Errno 2] No such file or directory: 'tmp'

Issue - State: closed - Opened by yipy0005 almost 3 years ago - 1 comment

#73 - Bump ipython from 7.16.2 to 7.16.3

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago - 1 comment
Labels: dependencies

#72 - More docs and some improvements

Pull Request - State: closed - Opened by alanwilter about 3 years ago - 1 comment

#71 - New_add_doc

Pull Request - State: closed - Opened by alanwilter about 3 years ago - 1 comment

#70 - Tttt

Pull Request - State: closed - Opened by alanwilter about 3 years ago - 1 comment

#69 - Add documentation

Pull Request - State: closed - Opened by alanwilter about 3 years ago - 1 comment

#68 - Full move to poetry

Pull Request - State: closed - Opened by alanwilter about 3 years ago - 1 comment