[gmx-users] MD Error after adding a unnatural amio acid
liucan1 at yahoo.com
Wed Jan 24 17:31:54 CET 2007
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?
Bond Angle Proper Dih.
Improper Dih. LJ-14
4.40414e+03 7.17452e+03 3.03251e+03
Coulomb-14 LJ (SR) Coulomb (SR) Coul.
4.01788e+04 2.57243e+05 -1.94251e+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
3173 14.01 3174 1.01 0.10000 0.15192
Constraint error in algorithm Shake at step 650187
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