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.
Mark
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