Discussions

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  Invoking martinize2 with and without the -dssp flag

  vaneerdf asked Jul 7, 2025 in Q&A · Unanswered

  

  

  

  

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  QUESTION: How can I martinize very big protein structures accurately? I've tried using martinize with structures with atoms >99999 and I received errors because it was unable to read the pdb file.

  Boupalik started Jul 15, 2024 in General

  

  

  

  

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  martinize2: Protein + Ligands

  fpontes22 asked Jun 9, 2025 in Q&A · Unanswered

  

  

  

  

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  Martinize2 error when calling DSSP

  wontfix

  Sean-S1225 asked Jun 4, 2025 in Q&A · Closed · Unanswered

  

  

  

  

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  martinize2 for martini22 and glycoprotein

  shilburg asked Apr 17, 2025 in Q&A · Unanswered

  

  

  

  

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  Molecule type in go_atomtypes.itp

  Vini161 started Apr 11, 2025 in General

  

  

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  POSRES_FC update

  Vini161 asked Nov 24, 2024 in Q&A · Closed · Unanswered

  

  

  

  

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  Residue numbering

  Vini161 started Feb 22, 2025 in General

  

  

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  Error with new Force Field

  rinkyimrk asked Dec 11, 2024 in Q&A · Closed · Answered

  

  

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  Multimer protein

  Vini161 asked Nov 23, 2024 in Q&A · Unanswered

  

  

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  Unexpected TER in martinize2 Production- protein with 4 subunits split into 7 ITPs with 3 unexpected TERs

  JingkaiZeng asked Oct 17, 2024 in Q&A · Unanswered

  

  

  

  

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  martinize2 -p backbone create NO restraints

  Toolxx asked Oct 15, 2024 in Q&A · Unanswered

  

  

  

  

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  Difficulty to martinize

  amiel-ab asked Sep 12, 2024 in Q&A · Answered

  

  

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  secondary structure file format

  John-zzh asked Jul 15, 2024 in Q&A · Unanswered

  

  

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  Coarse-graining of arbitrary protein sequences

  freakyacorn asked Jun 24, 2024 in Q&A · Unanswered

  

  

  

  

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  Post translational modification

  amiel-ab started May 7, 2024 in Ideas

  

  

  

  

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  Atomtype Q5 not found error -Go model simulation

  Asharuthra started May 24, 2024 in General

  

  

  

  

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  How to get the Martini CG of an AA polymer?

  pranoy-ray asked Mar 11, 2024 in Q&A · Answered

  

  

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  Coarse Grain a basic All-Atom structure of Polystyrene

  pranoy-ray asked Feb 23, 2024 in Q&A · Closed · Answered

  

  

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  DNA-protein sims in MARTINI 3

  agoliaei asked Jan 22, 2024 in Q&A · Answered

  

  

  

  

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  removing interactions (again)

  csbrasnett started Oct 5, 2023 in General · Closed

  

  

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  Adding palmitoyl chains to a protein

  mdoktorova asked Aug 24, 2023 in Q&A · Unanswered

  

  

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  redundant link in martini3001

  data

  fgrunewald started Jun 21, 2023 in General

  

  

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  Error when generate Martini topology and coordinates

  Clare-xiong announced Mar 22, 2023 in Announcements

  

  

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  Suggestion: "Mean field" histidine

  enhancement data feature-request

  KasperBuskPedersen announced Feb 8, 2023 in Announcements

  

  

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