[gmx-users] No bonds in *.top file

Dawid das addiw7 at googlemail.com
Mon Feb 29 22:11:35 CET 2016

Dear Gromacs Experts,

I run gmx pdb2gmx and it runs without any warnings or errors by the *.top
file does not
contain any bonds. The *.gro file is fine and all hydrogen atoms are added

Now I have discovered that when I get rid of calcium ions in my *.pdb file
I get proper
*.top file. But I don't want to get rid of them. How can I generate proper
*.top file
with my Calcium ions?
They are orginally part of the same chain (A) as the protein and water
When I changes this to B chain (calcium ions) it does not help.

Best wishes,
Dawid Grabarek

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