Dear all,
I perform parameterization for a terpene synthase's magnesium ions binding site (PDB ID: 6OFV, chain A), building a bonded model. And I have topology and coordinate files finally. But it goes wrong during minimization. The portion of the output file is as follows:
————————————
NSTEP ENERGY RMS GMAX NAME NUMBER
600 -2.5309E+07 2.6984E+10 6.8559E+12 OD1 1353
BOND = 8585.4915 ANGLE = 1006.2007 DIHED = 3823.9176
VDWAALS = 12025.1277 EEL = -184709.9835 HBOND = 0.0000
1-4 VDW = 1146.7754 1-4 EEL = ************* RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
700 -4.7347E+07 9.4961E+10 2.4127E+13 H2 5450
BOND = 8585.4911 ANGLE = 1006.2005 DIHED = 3823.9176
VDWAALS = 12025.1277 EEL = -184709.9836 HBOND = 0.0000
1-4 VDW = 1146.7754 1-4 EEL = ************* RESTRAINT = 0.0000
————————————
It seems that the corresponding aspartate residue and water molecule which are connected to the same magnesium ion cause structure distortion. Although I delete related bonds in the LEaP modeling, treating the bonds in a nonbonded way as suggested in the tutorial, it doesn't work well.
How can I fix this problem if I want to use a bonded model? Whether it is better to use harmonic restraints for all the coordination bonds in this specific situation?
The original files generated by MCPB.py are in the attachment.
Any suggestions are welcome. Thank you in advance.
Kind regards,
Zijian Huang
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Received on Wed Oct 19 2022 - 21:30:03 PDT
