[gmx-users] positional restraint

[Xavier Periole]

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

-- 
----------------------------------------------

   Xavier Periole - Ph.D.

   Dept. of Biophysical Chemistry / MD Group 
   Univ. of Groningen
   Nijenborgh 4
   9747 AG Groningen
   The Netherlands

   Tel: +31-503634329
   Fax: +31-503634800
   email: x.periole at chem.rug.nl
   web-page: http://md.chem.rug.nl/~periole
   
----------------------------------------------