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

[plmallip at mail.uh.edu]

Hi,

     There is no chance of steric clashes between 6151 & 6160. They are seperated by 12 A. ("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") I cannot build the missing residues without knowing the secondary structure. I am already running one simulation with built residues. But, my ultimate goal is to run dynamics with distance restraints.
 
       My sytem is an pentamer. Here is the toplogy file

; Include forcefield parameters
#include "ffG43a1.itp"

; Include chain topologies
#include "chnrc_A.itp"
#include "chnrc_B.itp"
#include "chnrc_C.itp"
#include "chnrc_D.itp"
#include "chnrc_E.itp"

; Include water topology
#include "spce.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound        #mols
Protein_A           1
Protein_B           1
Protein_C           1
Protein_D           1
Protein_E           1
SOL              55419
NA+              54


Thanks & regards,
Latha.

> > 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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> -- 
> ========================================
> 
> 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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