[gmx-users] Segmentation fault 4

[Tanos C. C. França]

Hi  Anton !!!!!!!!! 
It´s the protein docked with its cofactor and coenzyme. There are two
active sites with one cofactor and one coenzyme in each one. I have
already checked the structure in ProChek and everything is OK. I have
also performed one round of steep descent EM until emtol = 1000 and
further 1000 steps of cg.  I suspect that the problem is really the
molecules docked to the actives sites cause without then the dynamics
went well. I am looking now for any mistakes committed in the
parametrization and docking process.
            There is another detail in my job. I had to add 12 atoms of
Na+ to neutralize the system. Could this create any problem ?  If so, is
it acceptable to run the job without neutralize the system ???????
            Thanks a lot for you help !!!!!!!!!!!!!!!!
            Best
            Tanos C. C. Franca.
 
 
Christoph Freudenberger wrote:
> Tanos C. C. França wrote:
>>
>>             I am facing the problem of segmentation fault again
>> !!!!!!!!!!!! This time I am trying to perform a Position Restrained 
>> (PR) molecular dynamics (MD) of a crystallographic structure I have 
[...]
> You're using
> constraints         =  all-bonds
> with the default LINCS algorithm. Looks like your system gives coupled

> constraints that cannot be resolved by LINCS (check the manual about 
> that).
 
If it's just a protein, all-bonds & Lincs should work.
Perhaps there are strange things in your crystal structure.
Did you do EM before the MD? (You *must*!)
Have you checked the crystal structure with for example ProCheck?
 
            
            

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