From: Sunjoo Lee (
Date: Thu Jul 23 2009 - 13:25:46 CDT

I am trying to draw lipids and other small molecules, which are modeled by a
coarse-grained model.

The easiest way seemed to generate a pdb file with the connectivity.
All the bonding information was given at the end of a pdb file.
But I still do not see bonds connecting two interaction sites.
Could anyone tell me what the problem may be and how I can fix this problem?

The second method I would like to try is to use bonding information obtained
from a gmxdump file.
Could anyone explain more explicitly how I can use the bonding information
to draw bonds?

Thank you in advance