[gmx-users] reg bonds missing in the final pdb

[vidhya sankar]

dear Justin , Thank you for immediate valuable reply.

I have all bonds in my original PDB But after doing Dynamics I have converted .gro file to .pdb by trjconv_d tool
 In thsi pdb file some of the bonds Have been missed between the atoms though i am using constraints = all-bonds in .mdp files.
How to recover those bonds in my final .pdb .At the same time when i measure  distance between the atoms which are not connected,  using VMD it shows some distances 
 
I am not sure of my final pdb retain the bonds as original .pdb.

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