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

Justin A. Lemkul jalemkul at vt.edu
Mon May 16 04:35:28 CEST 2011

vidhya sankar wrote:
> 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.

Bonds are defined in the topology.  Bonds cannot break or form.  If it appears 
that bonds have broken this is simply a visualization artifact and may or may 
not be related to PBC.

See FAQ 9 and perhaps 11:




Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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