[gmx-users] Bonds break while Minimising using distance restraints

Justin A. Lemkul jalemkul at vt.edu
Tue Sep 2 00:27:16 CEST 2008

plmallip at mail.uh.edu wrote:
> Dear colleagues,
> I need to use simple distance restraints of 12.5 A between two CA atoms 
> of two residues. I am using the following lines in the .itp file
> #ifdef DDISRES
> [distance_restraints]
> ;ai   aj type index type' low   up1  up2  fac
> 1703 1712 1    0     1    11.5  12.0 12.5 1.0
> The first feww line of .mdp file for minimisation of protein alone is
> ; Preprocessing
> ;
> title               =  ${MOL}
> cpp                 =  /lib/cpp    ;Preprocessor
> define              = -DDISRES  ;For cg, and also steep

You are not actually applying your distance restraint.  If you have "#ifdef 
DDISRES," then you would have to "define = -DDDISRES" in the .mdp file.  What 
you probably meant to define was "#ifdef DISRES" in the topology.

>          After minimisation, the restarined residues & the adjacent 
> bonds break. This results in fragmnets - residues alone, peptide bond 
> alone and the rest of the protein. The distance restrained residues 
> seems to try to move towards each other (6.04 A after minimisation) and 
> this might have caused fragmentation. I tried to use various upper and 
> lower values for bond length so as to increase flexibility. But, still I 
> end up in the fragments.

Bonds don't break in classical MD, this is just an artifact of visualization, 
probably from nasty steric clashes within your structure.

>         Some of the suggestions in the archive says VMD doesn't show 
> bonds if they r above threshold value. When I checked the distances 
> between the atoms, one of them is really long CO-CA bond 3.23 A 
> (normally its 1.59A). This means the bond is no longer there.

No, the bond is there, VMD just isn't smart enough to see it :)  You are 
probably well on your way to an explosion if you try to constrain bond lengths 
with LINCS, however.


> I appreciate any suggestions in this regard.
> Thanks & regards,
> Latha.
> ------------------------------------------------------------------------
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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