[gmx-users] Coarse-Grain: GROMACS bond information to VMD

Mark Abraham Mark.Abraham at anu.edu.au
Mon Oct 19 16:38:33 CEST 2009

Thomas Schmidt wrote:
> Dear Omer,
> many thanks for your answer, but your solution doesn't work for me.
> We have Protein-Lipid models in the CG scale.
> Only if I replace all atom names in the PDB file through "CA" I can use
> the "trace" drawing method, but get also wrong atoms connected to each
> other. For example CG Beads with low distances to each other, e.g. in
> coarse-grained benzene rings, were not connected. I guess that this
> method is distance dependent, too, but in another way. :-)
> Does anybody else have a solution (...to put GROMACS bond information
> into VMD)?

No, but you can change the bond length heuristic VMD uses to guess where 
bonds are. See its manual or mailing list archives, I guess.


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