You probably want to take a look of the procedure documented in:
Molecular Dynamics of p53 DNA Binding Domain, /J. Phys. Chem./,
111:11538-11545, 2007.
All the best,
Ray
==========================================
Ray Luo, Ph.D.
Associate Professor in Computational
Biochemistry and Molecular Biophysics
Dept of Molecular Biology and Biochemistry
Dept of Biomedical Engineering
University of California, Irvine, CA 92697-3900
Email: rluo.uci.edu Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/rayl/
==========================================
xuemeiwang1103 wrote:
> Dear All:
> I used a general approach to model the zinc ion in my protein system.The method involves geometry optimization of the model system for active site zinc complex .In this model , two methyi imidazole , one water and two butyrate are used to represent the active site histidine and GLU respectively.Now I have got the parameters ,such as bond length,angle,resp charge.Maybe there is some wrong when I dealing with the charge,I only modified the charge of the atom which bond to the zinc ion in the lib that I copied from the Amino94.lib. And the total charge of the system is not integral.When I minimal my system.it always stop.By reference to the ArchiveŁ¬I konw there may be some wrong about the atom H1 5380 (H2O),may be the charge (H1 0.6056,O -1.0669,H2 0.4783).Could some one tell me how to deal with the charge I got form the simplely model and how can I solve the problem below?
> the output file:
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 3800 -1.0101E+07 3.1414E+09 9.4711E+11 H1 9280
>
> BOND = 19291.7720 ANGLE = 1437.9125 DIHED = 5523.9582
> VDWAALS = 43114.5412 EEL = -362398.2861 HBOND = 0.0000
> 1-4 VDW = 1932.9914 1-4 EEL = -9809591.5659 RESTRAINT = 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 3900 -1.1929E+07 4.4181E+09 1.3320E+12 H1 9280
>
> BOND = 19291.7717 ANGLE = 1437.9124 DIHED = 5523.9582
> VDWAALS = 43114.5412 EEL = -362398.2862 HBOND = 0.0000
> 1-4 VDW = 1932.9914 1-4 EEL = ************* RESTRAINT = 0.0000
>
>
>
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Received on Wed Jun 02 2010 - 14:00:03 PDT
