[gmx-users] Problem in .gro file

[faride badalkhani]

Dear all,

I am trying to simulate a hyperbranced polymer (a dendrimer) with gromacs.
Therefore, I have parametrized the GROMOS 53A6 FF, and executed pdb2gmx,
and got a command as follows:
"You have successfully generated a topology from : G3-Neutral.pdb
The Pamam force field and the spce water model are used."

But, when I open the G3-Neutral_processed.gro with VMD, it is in a strange
shape, and hasnt got the correct form af a dendrimer. It seems that it
annot realize the correct connections between residues in a branched
polymar such as dendrimer.

Your answers will be really helpful.
Thanks alot,
Farideh