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

[Justin A. Lemkul]

plmallip at mail.uh.edu wrote:
> 
> plmallip at mail.uh.edu wrote:
> 
> Hi Justin, thanks for your response. You are right. I get the following 
> message in the .job file
> 
> "Warning: 1-4 interaction between 6151 and 6160 at distance 1.387 which 
> is larger than the 1-4 table size 1.000 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding"
> 
> The atoms I restrained are 1703 & 1712 (6151 & 6160 atoms are also from 
> the same residues). The distance between them is 12 A (there are 14 
> missing residues in between). My aim is to use distance restraints, 
> without building missing residues in between. Is there any way I can 
> overcome this warning why minimizing the system?

It's very hard to say, because none of us knows what's in your system, topology, 
or how you built things :)

You have some type of nasty steric clash that's driving atoms 6151 and 6160 
apart.  Visualize the trajectory (.trr) to see if you can identify where things 
start to break down.  I don't know if the distance restraint has anything to do 
with the problem or not.

Is there a problem with building missing residues?  That might make life quite a 
bit easier in the long run.

-Justin

> 
> Thanks & regards,
> Latha.
> 
> 
>  > 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.
> 
> -Justin
> 
> 
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-- 
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Justin A. Lemkul
Graduate Research Assistant
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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