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

[Justin A. Lemkul]

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:

http://www.gromacs.org/Documentation/FAQs

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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