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My issue :<BR>
>> I want to do energy minimization on a loop that had been missing and was <BR>>>filled in by modloop, while freezing the rest of the protein. <BR>>> <BR>>> Before the minimization I have an SO4 ion and 135 water molecules from the <BR>>>crystallography around the protein. After the minimization the protein has <BR>>>been translated in the y direction away from the water and SO4. <BR>
<BR>
Xavier Periole wrote:<BR>>You might want to solvate your system before minimization ... the<BR>>modeled loop might appreciate some solvent around!<BR>
<BR>
Thanks Xavier, you were right! When I solvated before doing energy minimization<BR>
on the loop, the freeze group did not break apart.<BR>
<BR>
I wrote:<BR>
>> I’m confused about why part of the freeze group (the protein) is translated <BR>>>away from the other part (So4 + crystal water). This happens with both steep <BR>>>and l-bfgs.<BR>
<BR>
Xavier Periole wrote:<BR>
>.Could that simply be the result of periodic boundary conditions?<BR>
<BR>
I don't understand why the problem arose, why solvating before loop minimization <BR>
ameliorated it, and what it has to do with periodic boundary conditions. Could someone explain?<BR>
<BR>
Also, I still have an issue with how Gromacs is building my system. when I run <BR>
editconf -f $protName.gro -o box.gro -d 1.2 -bt dodecahedron<BR>
Gromacs places the solute in the top corner of the box, rather than<BR>
centering it in the box. Shouldn't it be in the center? What am I doing wrong?<BR>
<BR>
Thanks!<BR>
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