normal How to get bond connecting information for coarse grain models?

  • darrenphua
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4 weeks 1 day ago #8636 by darrenphua
Are there any scripts available for automatically providing the CONECT records that i can use to visualize bonds between beads?

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4 weeks 1 day ago #8637 by riccardo
I'm not sure about getting the CONECT directives in a pdb but if you are using VMD you can use cg_bonds to visualize the bonds in the CG models, see cgmartini.nl/index.php/tools2/visualization .
Note, use "cg_bonds-v5.tcl" for GROMACS versions from 5.x onwards.

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4 weeks 1 day ago #8638 by darrenphua
Are there alternatives besides VMD? Im having difficulty understanding how to operate it on windows platform because it seem the command line language is different.

In MARTINI lipids tutorial, there were CONECT records provided i think, so it made visualizing it in any software that recognises CONECT records much easier.

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6 days 22 hours ago #8655 by peterkroon
gmx editconf can create PDBs with CONECT records, if you give it a tpr file.

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