The HADDOCK category is meant for discussing any topic related to the use of the HADDOCK software, either as a local installation or via the <a href="http://haddock.science.uu.nl/services/HADDOCK2.2">HADDOCK web portal</a>. For details about HADDOCK please refer to <a href="http://www.bonvinlab.org/software/haddock2.2">http://www.bonvinlab.org/software/haddock2.2</a><br>Feel free to create new topics related to your questions!
BioExcel webinar: Integrative modelling of biomolecular complexes with HADDOCK
Active Residues/Ambiguous interaction restraints
Pdb file contains an unknown amino acid or nucleic acid base U
Protein protein docking
Protein and peptide-dna complex docking
Docking membrane ions and water
Protein exceeds max number of atoms
Secondary structure prediction
Scoring interface histidine
Multibody docking active sites?
<a href="http://www.gromacs.org/">GROMACS</a> is a free and open-source software suite for high-performance molecular dynamics and output analysis. It primarily targets bio-molecular simulations of thousands to millions of atoms, described by particle-based classical mechanics force fields. These simulations integrate the Newtonian equations of motion for billions of time steps, which permits scientists to understand behaviour on experimentally relevant time scales. <br>
Moving atoms between repartition and force evaluation
BioExcel Webinar #2: Performance tuning and optimization of GROMACS webinar
AMBER force field
Regarding minimization of edited structures
The CPMD category is meant for discussing topics related to the use of the <a href="http://www.cpmd.org">CPMD</a> software in biological oriented applications, and in particular its QM/MM interface
QMMM with other solvent like alcohol
This is the help forum for DISVIS, a <a href="http://github.com/haddocking/disvis">software</a> and <a href="http://milou.science.uu.nl/services/DISVIS">web portal</a> that allows you to visualizes and quantify the information content of distance restraints between macromolecular complexes
BioExcel Webinar: Robust solutions for cryoEM fitting and visualisation of interaction space (2017-02-15)
DisVis web portal 2.0
Release of the DISVIS web portal
This is the help forum for POWERFIT, a <a href="http://github.com/haddocking/powerfit">software</a> and <a href="http://milou.science.uu.nl/services/POWERFIT">web portal</a> that allows you to automatically fits high-resolution atomic structures in cryo-EM densities.
Webinar: Robust solutions for cryoEM fitting and visualisation of interaction space (2017-02-15)
PowerFit web portal 2.0
Release of the POWERFIT web portal
Integrative Modelling IG
This category is for all discussions related Integrative Structural Biology and Modelling, offering a forum to discuss various approaches and software. Please also register at <a href="http://bioexcel.eu/interest-groups">http://bioexcel.eu/interest-groups</a> to receive our newsletter.
BioExcel webinar: Robust solutions for cryo-EM fitting and visualisation of interaction space
BioExcel Webinar #7: PRODIGY, a web server to predict binding affinities in protein-protein complexes
Follow-up on "Webinar #1 Integrative modelling of biomolecular complexes with HADDOCK"
Announcing the POWERFIT webserver
Announcing the DISVIS webserver
Why this group and a few questions for you
Performance Tuning and Optimisation IG
This category is for all discussions related to the Performance Tuning & Optimisation Interest Group that don't relate directly to one specific code. It's still best to post GROMACS-specific questions to the GROMACS category. You must be a member of the Performance Tuning IG to post here, but all posts are world-readable.
Molecular Dynamics Novice Users IG
This category is for discussions amongst members of the Molecular Dynamics Novice Users Interest Group that do not relate directly to GROMACS, HADDOCK or CPMD. If your question relates to one of these codes, please use the code-specific forums on this site.
CMIP titration service failure
PATC Simulation Environment for Life Sciences 2017
BioExcel Webinar #3: Atomistic Molecular Dynamics Setup with MDWeb
Free Energy IG
This category is for all discussions related to the Free Energy Interest Group. Its primary audience is members of the IG but this forum is open for anyone to contribute.
Follow-Up from Webinar: Mutation free energy calculations with pmx
This category is for all discussions related to the <a href="http://bioexcel.eu/interest-groups/">Workflows Interest Group</a>. Its primary audience is members of the IG but this forum is open for anyone to contribute.
Follow up on "Large-scale analytical workflows on the cloud using Galaxy and Globus"
Musings on GROMACS and workflow description integration
Welcome to ask.bioexcel.eu
About a simple interpretation of the Haddock results
What are the units of energies of HADDOCK?
Protein Structural changes Because of Single Mutation
Discussion about this site, its organization, how it works, and how we can improve it.
Add support for inline email replies
New topic to test replies