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Martinize.py empty output
- ak418
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3 years 7 months ago #8687
by ak418
Martinize.py empty output was created by ak418
Hello, I am trying to use the martinize.py script to "martinize" glycerol, ferulic acid, sinapic acid, and 16-hydroxy fatty acids. For instance when I run the fatty acid (juniperic acid) I get this in the .itp output file
#include "martini.itp"
[ system ]
; name
Martini system from juniperic1.pdb
[ molecules ]
; name number
~
This happens with all the other files. I'm not sure where the problem lies, the PDB files are fine and I tried different ones (converted .mol to pdb with OpenBabel, SMILES to PDB, etc) but the result is the same.
#include "martini.itp"
[ system ]
; name
Martini system from juniperic1.pdb
[ molecules ]
; name number
~
This happens with all the other files. I'm not sure where the problem lies, the PDB files are fine and I tried different ones (converted .mol to pdb with OpenBabel, SMILES to PDB, etc) but the result is the same.
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- riccardo
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3 years 7 months ago #8689
by riccardo
Replied by riccardo on topic Martinize.py empty output
Martinize.py only works for protein (or DNA - for that, there's a custom martinize-DNA.py version).
Martini models for small molecules require some manual work. Here's the tutorial for Martini 2: cgmartini.nl/index.php/tutorials-general...ng-new-molecule-gmx5 (and we recently made a tutorial for making small molecules models with Martini 3, see here: cgmartini.nl/index.php/martini-3-tutoria...a-new-small-molecule ).
Martini models for small molecules require some manual work. Here's the tutorial for Martini 2: cgmartini.nl/index.php/tutorials-general...ng-new-molecule-gmx5 (and we recently made a tutorial for making small molecules models with Martini 3, see here: cgmartini.nl/index.php/martini-3-tutoria...a-new-small-molecule ).
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- ak418
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3 years 6 months ago #8694
by ak418
Replied by ak418 on topic Martinize.py empty output
Has anyone done a parametrization of glycerol? I see there are acylglycerols available, can I use those as a starting template?
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