normal Atomtype mismatch : Martini 3 beta vs Martini 3

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1 year 7 months ago #9053 by sayantan0510
Hello,

I am a relatively new explorer of martini and CG simulations and trying to model a peptide by using Martini 3.0.

So I used the "martinize" provided with the beta version and included 'martini_v3.0.b.3.2.itp' in the topology file. Things worked out fine.

However, when I use the 'martini_v3.0.0.itp' provided in the 'New Downloads' there are several atom name mismatch during grompp, for example, Qd, Qn etc. to name a few.

This is probably expected assuming there are changes in the atomtype in the non-beta version but is there an easy fix? Is the non-beta 'martinize.py' available? Or, one can use the one provided with the beta version and still manages to use the non-beta .itp files?

Thank you for your time.

Best regards,
Sayantan

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1 year 7 months ago #9055 by riccardo
Hi. The M3 beta version and the official release (v3.0.0) have indeed some different bead types. So you should martinize molecules with the appropriate version in order for it to be run with that version.

You can get the latest martinize2 version from github: github.com/marrink-lab/vermouth-martinize . It handles generation of Martini models for proteins with the latest version (v3.0.). The tool is still being finalized though so the documentation is not really comprehensive yet. You can find some on the M3 paper's supplementary info, section H ( static-content.springer.com/esm/art%3A10..._1098_MOESM1_ESM.pdf ). There have been also a few discussions in this forum and among issues raised for martinize2 on GH ( github.com/marrink-lab/vermouth-martinize/issues ).

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