[gmx-users] Issue with the PDB generated after topology

[Nikhil Maroli]

Hi,

So you're saying you are able to see the full proteins after salvation but
not able to see it as Chain A and Chain B?. If that's the situation there
is nothing wrong here, *.gro file and *.pdb file representations are
different.
If you too much concern about these verify by converting the *.gro file to
*.pdb and see all the aa are there.