<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:arial,helvetica,sans-serif;font-size:10pt"><div style="font-family: arial,helvetica,sans-serif; font-size: 10pt;"><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><div style="font-family: arial,helvetica,sans-serif; font-size: 10pt; color: rgb(0, 0, 0);"><div>Hi.<br><br>I'm trying to subject a metalloprotein bound to cadmium to
a molecular dynamics. I've defined the cadmium ion in the atom type
parameter file (ffGa56a6.atp) and residue database (ffG53a6.rtp). And
the bond length and bond
angle between the cadmium and sulphur of the metalloprotein had been
define in the force field file, too (ffG53a6abon.itp). As special bond
is expected to be formed between the sulphur of cysteine and the cadmium
ions, I've added the relevant information into specbond.dat.<br>
<br>But when I
run the pdb2gmx, there is no entries in the [ bonds ] and [ angles ] for
those bond length and bond angle. And of course, as there is no entries
in those parameter, there was no cadmium-thiolate bond observed when I
visualised the structure using pymol. So, does that mean
that I would need to
add them on manually? <br><br>To proceed with my simulation, I added the
values in [ bonds ] and [ angles ] manually. And as I do not have the
relevant dihedral angle value from the literature, I've deleted those
entries in my topology file and continue to prepare and subject the
protein to energy minimization. During EM, the potential energy of the
system started to remain constant at step 124 and eventually steepest
descents converged to machine precision in 128 steps with the maximum
force is on atom 279 which would be one of the cadmium ions in the
system. When I visualised the system, one water molecule was found to
attached with atom 279, so I deleted that water molecule and subject the
system to em again. Yet the same thing occur after running for 49
steps. What had gone wrong with my system? Is that cadmium molecule had
been running too far until it has gone out of the protein as water
molecule are not suppose to come into the protein. <br>
<br>Any suggestion is welcomed.<br><br>Thanks in advance.<br><br>Regards,<br>Joyce</div>
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