Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / marrink-lab/vermouth-martinize issues and pull requests

#633 - this is a problem about martinize2 can't run.

Issue - State: closed - Opened by chemcrazy 13 days ago - 4 comments

#632 - Can Martinize2 working on other molecules besides protein?

Issue - State: open - Opened by hliu56 15 days ago - 1 comment

#631 - Rtp parser - Abandon all hope, ye who review here

Pull Request - State: open - Opened by pckroon 15 days ago - 6 comments

#629 - Pylint update

Pull Request - State: closed - Opened by pckroon 24 days ago - 1 comment

#628 - IDP go interactions and secondary structure

Pull Request - State: open - Opened by csbrasnett 24 days ago

#627 - -go-moltype arguement not used

Issue - State: closed - Opened by chenyuwai 26 days ago - 5 comments

#626 - link across annotations

Issue - State: closed - Opened by csbrasnett 30 days ago

#625 - Log disulfide bridges

Pull Request - State: closed - Opened by csbrasnett about 1 month ago - 1 comment

#625 - Log disulfide bridges

Pull Request - State: closed - Opened by csbrasnett about 1 month ago - 1 comment

#624 - topol headers for go files

Issue - State: open - Opened by csbrasnett about 1 month ago

#624 - topol headers for go files

Issue - State: open - Opened by csbrasnett about 1 month ago

#623 - Custom molname

Pull Request - State: open - Opened by csbrasnett about 1 month ago - 9 comments

#622 - change elastic network default

Pull Request - State: closed - Opened by csbrasnett about 1 month ago

#622 - change elastic network default

Pull Request - State: closed - Opened by csbrasnett about 1 month ago

#621 - scfix behaviour change

Pull Request - State: closed - Opened by csbrasnett about 1 month ago - 5 comments

#621 - scfix behaviour change

Pull Request - State: closed - Opened by csbrasnett about 1 month ago - 5 comments

#620 - write cysteine bridge identification to log

Issue - State: closed - Opened by csbrasnett about 1 month ago

#617 - martinize2 -p backbone create NO restraints

Issue - State: closed - Opened by Toolxx about 1 month ago - 4 comments

#617 - martinize2 -p backbone create NO restraints

Issue - State: closed - Opened by Toolxx about 1 month ago - 4 comments

#616 - first draft of martinize2 command tutorials

Pull Request - State: open - Opened by csbrasnett about 2 months ago - 10 comments

#615 - water biasing not auto identified from secondary structure

Issue - State: open - Opened by csbrasnett about 2 months ago
Labels: easy

#615 - water biasing not auto identified from secondary structure

Issue - State: open - Opened by csbrasnett about 2 months ago
Labels: easy

#613 - read secondary structure from file

Issue - State: open - Opened by csbrasnett 2 months ago - 4 comments
Labels: enhancement, easy

#613 - read secondary structure from file

Issue - State: open - Opened by csbrasnett 2 months ago - 4 comments
Labels: enhancement, easy

#611 - Rework the deploy pipeline

Pull Request - State: closed - Opened by pckroon 3 months ago

#610 - Add HIS(charmm)->HSE(martini22) mapping

Pull Request - State: closed - Opened by pckroon 3 months ago

#609 - Visualizing Go bonds

Issue - State: open - Opened by Lp0lp 3 months ago - 3 comments

#607 - secondary structure file format

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

#604 - Autogenerate modification auto-mappings

Pull Request - State: open - Opened by pckroon 5 months ago - 8 comments

#603 - -govs-include no longer present?

Issue - State: closed - Opened by BartBruininks 6 months ago - 2 comments

#602 - fix error raising for mod not found

Pull Request - State: closed - Opened by csbrasnett 6 months ago

#601 - isomorphism propagation

Issue - State: open - Opened by csbrasnett 6 months ago - 3 comments
Labels: enhancement

#599 - interaction removal

Issue - State: closed - Opened by csbrasnett 6 months ago - 3 comments

#598 - Atomtype Q5 not found error -Go model simulation

Issue - State: closed - Opened by Asharuthra 6 months ago - 2 comments

#596 - External EN bonds itp

Pull Request - State: open - Opened by csbrasnett 7 months ago - 2 comments

#595 - Issue 584

Pull Request - State: open - Opened by pckroon 7 months ago

#594 - Corse graining lipids molecules and ions

Issue - State: open - Opened by Senweiuoa 7 months ago - 3 comments
Labels: data

#593 - Idp go

Pull Request - State: closed - Opened by csbrasnett 7 months ago - 8 comments

#592 - Error While Martinizing "AssertionError"

Issue - State: open - Opened by Harshitasahni 7 months ago - 1 comment

#591 - Idp bugfix

Pull Request - State: closed - Opened by csbrasnett 7 months ago

#590 - GO IDP bugfix

Pull Request - State: closed - Opened by csbrasnett 7 months ago - 3 comments

#589 - Lazy merge

Pull Request - State: closed - Opened by csbrasnett 7 months ago - 2 comments

#588 - martinize2 command not found error:after adding the full path in bashrc

Issue - State: closed - Opened by Asharuthra 7 months ago - 2 comments

#587 - Lazy merging?

Issue - State: closed - Opened by csbrasnett 8 months ago - 1 comment
Labels: enhancement

#586 - Every Job Ran for Martinize2 is Killed/No Residues Recognized

Issue - State: closed - Opened by zamydm 8 months ago - 9 comments
Labels: question, user

#585 - Expose Go model `backbone` and `atomname` in `add_virtual_sites`

Issue - State: open - Opened by Lp0lp 8 months ago - 1 comment
Labels: enhancement

#584 - Replace entire link instead of potential by potential

Issue - State: open - Opened by Lp0lp 8 months ago - 3 comments
Labels: enhancement

#582 - Doc new

Pull Request - State: closed - Opened by fgrunewald 8 months ago - 2 comments

#581 - Fix 580

Pull Request - State: closed - Opened by fgrunewald 8 months ago

#580 - Slient dropping of edge attributes

Issue - State: closed - Opened by fgrunewald 8 months ago - 1 comment
Labels: bug

#577 - Windows issues

Pull Request - State: open - Opened by pckroon 9 months ago

#576 - SEQRES parsing

Pull Request - State: open - Opened by csbrasnett 9 months ago - 1 comment

#573 - Issue with new MDTraj -dssp flag

Issue - State: closed - Opened by KasperBuskPedersen 9 months ago - 3 comments

#572 - Flank the wildcard SecStruct sequence with dots

Pull Request - State: closed - Opened by pckroon 10 months ago - 2 comments

#571 - Log a helpful message when an element is not present in the ATOM_MASS dict

Pull Request - State: closed - Opened by pckroon 10 months ago - 1 comment

#570 - parameterizing ATP and MG+

Issue - State: closed - Opened by Nancyarvin 10 months ago - 9 comments

#569 - BB-BB(-1)-BB(+1)-SC improper dihedral definition

Issue - State: closed - Opened by WangLiguo-kyrie 10 months ago - 5 comments

#567 - HIS mapping issue when -ff is set to martini22

Issue - State: closed - Opened by tnozturk 11 months ago - 6 comments

#566 - Martini 2.2 topologies for alpha-helical peptides are still incorrect

Issue - State: closed - Opened by Ladme 12 months ago - 8 comments

#565 - Multiple mutate fixes

Pull Request - State: closed - Opened by csbrasnett 12 months ago - 12 comments

#564 - How to deal with the different protonation states in martinize2?

Issue - State: closed - Opened by yuqingxiong96 12 months ago - 2 comments

#563 - add lipidations

Issue - State: open - Opened by fgrunewald 12 months ago
Labels: data

#562 - some error about dssp

Issue - State: closed - Opened by bdx114514 about 1 year ago - 2 comments

#561 - Issue 560

Pull Request - State: closed - Opened by pckroon about 1 year ago

#560 - Incorrect Martini 2.2 topologies for alpha-helical peptides

Issue - State: closed - Opened by Ladme about 1 year ago - 4 comments
Labels: bug

#559 - -el fix

Pull Request - State: closed - Opened by csbrasnett about 1 year ago - 9 comments

#558 - Wrong exclusions for charged termini in 2.2P

Issue - State: closed - Opened by yummy-hat about 1 year ago - 5 comments
Labels: bug, data

#557 - Instabillity in large proteins

Issue - State: open - Opened by fgrunewald about 1 year ago
Labels: data

#556 - add warning when mod not found

Pull Request - State: closed - Opened by csbrasnett about 1 year ago - 3 comments

#555 - Cleanup to Go implementation

Pull Request - State: closed - Opened by Lp0lp about 1 year ago - 2 comments

#554 - parse_pragma cannot handle #include in .itps files which are in #include in the top

Issue - State: open - Opened by BartBruininks about 1 year ago - 3 comments
Labels: enhancement, help wanted, parser

#553 - Raise warning if mutation not found

Issue - State: closed - Opened by csbrasnett about 1 year ago - 9 comments

#552 - First draft of a ProcessorPipeline

Pull Request - State: open - Opened by pckroon about 1 year ago
Labels: hacktoberfest-accepted

#550 - Implementation of the Martini3 Go-model

Pull Request - State: closed - Opened by fgrunewald about 1 year ago - 37 comments
Labels: hacktoberfest-accepted

#549 - Make sure DATA_PATH is always a pathlib.Path

Pull Request - State: closed - Opened by pckroon about 1 year ago
Labels: hacktoberfest-accepted

#547 - Use MDTraj dssp

Pull Request - State: closed - Opened by pckroon about 1 year ago - 3 comments
Labels: hacktoberfest-accepted

#546 - Replace deprecated pkg_resources with new importlib

Pull Request - State: closed - Opened by pckroon about 1 year ago
Labels: hacktoberfest-accepted

#545 - Documentation

Pull Request - State: closed - Opened by pckroon about 1 year ago - 3 comments
Labels: publication

#544 - fix pdb box

Pull Request - State: closed - Opened by fgrunewald about 1 year ago

#543 - Networkx 3

Pull Request - State: closed - Opened by pckroon about 1 year ago

#542 - quick fix doc

Pull Request - State: closed - Opened by fgrunewald about 1 year ago

#541 - test sphinx version

Pull Request - State: closed - Opened by fgrunewald about 1 year ago

#540 - Building Docs Fails

Issue - State: closed - Opened by fgrunewald about 1 year ago - 6 comments

#538 - The sequence length does not match the number of residues

Issue - State: open - Opened by DoubleSheep2 over 1 year ago - 7 comments

#537 - add box attribute to molecule and propagate from pdb parser

Pull Request - State: closed - Opened by fgrunewald over 1 year ago - 3 comments

#536 - Add support for oxDNA file parsing

Pull Request - State: open - Opened by jan-stevens over 1 year ago

#535 - martinize2 fails to detect newly parameterizing residues

Issue - State: closed - Opened by mdsptnlip over 1 year ago - 12 comments
Labels: FAQ

#534 - Enhancement: Leave structural ions in file

Issue - State: open - Opened by KasperBuskPedersen over 1 year ago - 6 comments
Labels: enhancement

#533 - System builder for 100 chains - comment line too long for grompp

Issue - State: open - Opened by kesavanekambaram over 1 year ago - 14 comments
Labels: bug

#532 - small lint

Pull Request - State: closed - Opened by fgrunewald over 1 year ago - 3 comments

#531 - Modifications Missing

Issue - State: open - Opened by fgrunewald over 1 year ago
Labels: data

#530 - Generating ITP file for use with create_goVirt.py

Issue - State: open - Opened by yummy-hat over 1 year ago - 5 comments
Labels: bug, easy

#529 - add modifications for all protonation states

Pull Request - State: closed - Opened by fgrunewald over 1 year ago - 12 comments