[gmx-users] positional restraint

[David]

On Tue, 2004-11-30 at 22:48 +0530, Alok wrote:
> hello Xavier and David,
>                                       I am really sorry for the mistake 
> i made with my previous mail.The residue in question is really ASN.And 
> the OD1 atom is not protonated as i said in my previous mail.It was a 
> blunder mistake on my part to say so.The  H-OD1 distance mentioned is 
> actually the distance between OD1  and the backbone Hydrogen 'H' of ASN. 
> And the distances mentioned is in Angstrom not in nanometer.

If it was O-OD1 distance in the crystal it must have been ASP instead of
ASN. Crystallographers cannot distinguish the two and sequence
information can be flaky at times too.


>                                      So coming back to my main question 
> about positional restraint.As I have shown the data that even with very 
> high force constant value (100000),there still is marked change in the 
> distances between the atoms.And the atoms are not freezed as u have 
> mentioned.Please shed some light into the whole issue.
>                    Sorry for the mistake :( with my previous mail.
>                                                                         
>                      Thank you,
>                                                                         
>                       Alok Jain
> Xavier Periole wrote:
> 
> > David wrote:
> >
> >> On Tue, 2004-11-30 at 01:32 +0530, Alok wrote:
> >>  
> >>
> >>> hello David and Xavier,
> >>>                         Thanks for all your responses to my previous
> >>> mails.I am sorry,I still have to bother you with
> >>> some more queries about the constraint.In the
> >>> process i would also like to answer few questions
> >>> u have asked in your responding mails.
> >>>
> >>> What is the range of differences you observe ?? Is it for the 
> >>> restrained
> >>> part or the rest of the protein ?
> >>>
> >>> The Observed distance difference is for the restrained part (the atoms
> >>> from the constrained residue).I have not checked the distance 
> >>> difference
> >>> between the other atoms of the protein as i expect it to vary anyway 
> >>> since
> >>> i am constraining only one residue in my protein.
> >>>
> >>> I present below data of distances (in Angstrom) between atoms of my
> >>> constained residue for the crystal structure as well as for the output
> >>> after Energy minimization using different Force constant.
> >>>
> >>>
> >>>                                     (Force Constant)
> >>>         Crystal      1000            10000              100000
> >>> O-OD1    2.58         3.17            2.87               2.66
> >>>   
> >>
> >> Is your OD1 protonated? It should...
> >>  
> >>
> > It seems to me that this residue is a ASN, since it contains OD1 and 
> > ND2. So I do not see why
> > the OD1 should be protonated. I must be missing something !
> > Although the distance is really small and should be a H-bond, which 
> > explain certainly why David
> > suggested that the OD1 should be protonated. That is my guess.
> > Another solution is that the X-ray attributed the density of ND2 to 
> > OD1 and vis versa, That happens
> > as the two atoms a not nesseraly easily discernable !
> >
> >>  
> >>
> >>> O-HD21   4.86         5.27            5.13               4.95
> >>> O-HD22   4.75         5.35            5.06               4.83
> >>> H-OD1    4.73         4.76            4.75               4.75
> >>> N-HD21   4.62         4.57            4.74               4.71
> >>> N-HD22   5.58         5.62            5.65               5.62
> >>> H-ND2    4.94         4.66            4.80               4.87
> >>>
> >>> As we can observe even after value of 1000000,the atoms have not 
> >>> freezed
> >>> as u have mentioned in your mail.
> >>>
> >>> my corresponding ".mdp " file for EM is as follows:
> >>>
> >>> cpp                 =  /lib/cpp
> >>> define              =  -DFLEXIBLE
> >>> constraints         =  none
> >>> integrator          =  steep
> >>> nsteps              =  10000
> >>> ;
> >>> ;    Energy minimizing stuff
> >>> ;
> >>> emtol               =  200
> >>> emstep              =  0.01
> >>> nstcgsteep          =  1000
> >>>
> >>> nstcomm             =  1
> >>> ns_type             =  grid
> >>> rlist               =  1.0
> >>> rcoulomb            =  2.0
> >>> rvdw                =  1.2
> >>> Tcoupl              =  no
> >>> Pcoupl              =  no
> >>> gen_vel             =  no
> >>>
> >>> If I am not able to freeze the atoms even after such high Force 
> >>> Constant,
> >>> then i am going wrong some where as you have suggested.Can you please
> >>> suggest the possible reason for the problem and would be thankfull 
> >>> if you
> >>> can shed some light into the possible solution.
> >>>
> >>>   
> >>
> >
> > XAvier
> >
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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