[gmx-users] positional restraint

Xavier Periole x.periole at chem.rug.nl
Wed Dec 1 15:25:10 CET 2004

David wrote:

>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
>>>>>                                    (Force Constant)
>>>>>        Crystal      1000            10000              100000
>>>>>O-OD1    2.58         3.17            2.87               2.66
This O-OD1 distance clearly indicates that if it so a H-bond must be 
between these
two atoms. If you have to apply so strong constrains is because two 
oxygen (of this kinds)
separated by this distance is not stable at all. Must be some 
compensation somewhere. An
H-bond may be. This is not possible as the residue is an ASN in this 
1) If we consider that the sequence is correct you should try to 
exchange the OD1 with ND2, which
would create an H-bond between O (backbone) and ND2. That is reasonable 
as I mentioned before
the OD1 and ND2 in structures are often mis-attributed, as O and N are 
very density like. I personaly
observed several ASN flipping within 10-20 ps and stay stable for the 
rest of the simulation. A detail
examination of the surounding atoms of the ASN in general explaion this 
flipping easily.
2) the crystallographers messed up there sequence and you got an ASP 
instead of an ASN.



   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

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