[gmx-users] positional restraint

Alok alokjain at iitk.ac.in
Wed Dec 1 20:20:23 CET 2004

Hello Xavier and David,
                                       Thank you both for all your 
responses to my queries.May be the residue is in fact asp and not asn or 
the atoms OD1 and ND2 are interchanged.So we are to conclude at this 
stage that the position restraint is not working efficently for this 
residue because of these reasons.May be we will trying restraining a 
differnet reisdue and back to you.Thank you once again.
                                               Alok Jain


Xavier Periole wrote:

> 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 
> conformation.
> Solutions:
> 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

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