[gmx-users] MD Error after adding a unnatural amio acid

yuemin liu liucan1 at yahoo.com
Wed Jan 24 17:31:54 CET 2007

Hi Everyone,

I once talked about this before and have new problem
now. The new group was successfully attached to the
protein, but problem comes during the process of MD.
The error messages are always like the following with
either new linkage broken or a neighboring Hydrogen
flying away. Parameters except for partial charge are
perfectly okay. The partial charges from HF
calculations even made it worse, because of different
scheme with gmx. I also tried to partition the new
bulky group into small fragments when T-coupling, but
did not help. I am wondering what the reasons are. Is
the new group too big? What is the alternative to
assign partial charge in gmx other than PRODRG?


Liu, Yuemin
    Energies (kJ/mol)
           Bond          Angle    Proper Dih. 
Improper Dih.          LJ-14
    4.40414e+03    7.17452e+03    3.03251e+03   
2.44614e+03    2.21377e+03
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul.
recip.      Potential
    4.01788e+04    2.57243e+05   -1.94251e+06  
-2.87497e+05   -1.91331e+06
    Kinetic En.   Total Energy    Temperature Pressure
    3.45332e+05   -1.56798e+06    2.99118e+02  

Shake did not converge in 1000 steps
    i     mi      j     mj      before       after  
should be
 3173  14.01   3174   1.01     0.10000     0.15192    
Constraint error in algorithm Shake at step 650187

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