Dear all,<div><br></div><div>I am attempting to keep a Zn ion in place in a zinc finger motif using distance restraints to the coordinating cysteine residues. The zinc is structural and not catalytic, and it was suggested from this list that using distance restraints should suffice without the need for reparameterization. </div>
<div><br></div><div>Unfortunately after several tries the distance restraints don't appear to be applied after 100 ps of isothermal-isochoric equilibration, however it did seem to work for the minimization step. My topology file contains the following:</div>
<div><br></div><div><div><font face="'courier new', monospace">#ifdef DISRES</font></div><div><font face="'courier new', monospace">[ distance_restraints ]</font></div>
<div><font face="'courier new', monospace">; ai aj type index typeâ low up1 up2 fac</font></div><div><font face="'courier new', monospace"> 13082 5576 1 0 1 0.0 0.23 0.3 10000.0</font></div>
<div><font face="'courier new', monospace"> 13082 5604 1 1 1 0.0 0.23 0.3 10000.0</font></div><div><font face="'courier new', monospace"> 13082 5959 1 2 1 0.0 0.23 0.3 10000.0</font></div>
<div><font face="'courier new', monospace"> 13082 5993 1 3 1 0.0 0.20 0.3 10000.0</font></div><div><font face="'courier new', monospace">#endif</font></div>
<div><br></div><div>and my .mdp file has the following two lines inserted:</div><div><br></div><div><font face="'courier new', monospace">define = -DDISRES ; distance restrain the protein</font></div>
<div><font face="'courier new', monospace">disre = simple ; Enable Distance Restraints</font></div><div><font face="'courier new', monospace"><br>
</font></div><div><font face="arial, helvetica, sans-serif">I first attempted to use small factors to multiply the restraints, 1, 2, 10, but nothing seemed to be working so I just put an extreme value of 10,000 to ensure the energy contribution from the restraints would dominate and keep the zinc in place, but that still didn't seem to do the trick which makes me think that there's some other error I'm missing. I checked my .gro file to ensure that the atom indices were correct and they are. I also have ensured that the zinc ion and coordinating cysteines are part of the same chain. </font><span style="font-family:arial,helvetica,sans-serif">The zinc appears to move by about 4 Å to be coordinated by a nearby glutamate instead.</span></div>
<div><font face="arial, helvetica, sans-serif"><br></font></div><div><font face="arial, helvetica, sans-serif">Any ideas on why the restraints don't seem to be working?</font></div>
<div><font face="arial, helvetica, sans-serif"><br></font></div><div><font face="arial, helvetica, sans-serif">Thanks,</font></div><div><font face="arial, helvetica, sans-serif">Tom</font></div>
<br clear="all"><br>--<br>Thomas D. Grant<br>Graduate Research Assistant<br>Hauptman-Woodward Medical Research Institute<br>700 Ellicott St.<br>Buffalo, NY 14203<br><br>
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