On Sat, 26 Jan 2008 21:40:20 -0800
Patricia Francis-Lyon <[EMAIL PROTECTED]> wrote:
I want to do energy minimization on a loop that had been missing and was
filled in by modloop, while freezing the rest of the protein.
Before the minimization I have an SO4 ion and 135 water molecules from the
crystallography around the protein. After the minimization the protein has
been translated in the y direction away from the water and SO4.
You might want to solvate your system before minimization ... the
modeled loop might appreciate some solvent around!
My freeze group is :
0 & ! 15 which is System and not loop.
I’m confused about why part of the freeze group (the protein) is translated
away from the other part (So4 + crystal water). This happens with both steep
and l-bfgs.
Could that simply be the result of periodic boundary conditions?
Thanks for your help!
Patricia Francis-Lyon
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-----------------------------------------------------
XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
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