How to get bond connecting information for coarse grain models?

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darrenphua
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3 years 9 months ago #8636 by darrenphua

How to get bond connecting information for coarse grain models? was created 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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riccardo
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3 years 9 months ago #8637 by riccardo

Replied by riccardo on topic How to get bond connecting information for coarse grain models?

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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darrenphua
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3 years 9 months ago #8638 by darrenphua

Replied by darrenphua on topic How to get bond connecting information for coarse grain models?

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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peterkroon
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3 years 8 months ago #8655 by peterkroon

Replied by peterkroon on topic How to get bond connecting information for coarse grain models?

gmx editconf can create PDBs with CONECT records, if you give it a tpr file.

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How to get bond connecting information for coarse grain models?