AW: vmd-l: SangbaeLee: question about pbc wrap

From: Norman Geist (
Date: Fri Aug 30 2013 - 02:15:30 CDT

Hi Lee,


please remember that if your protein unfolds that large that it will not
entirely fit into the box, there must be long bonds artifacts due the
wrapping, even if you centered the protein.


Norman Geist.


Von: [] Im Auftrag von
Lee, Sangbae
Gesendet: Donnerstag, 29. August 2013 20:12
Betreff: vmd-l: SangbaeLee: question about pbc wrap


Hi, VMD.

Now, I'm trying to analyze anton trajectories (converted to dcd file).

Using tcl command like "pbc wrap -centersel "protein" -center com -compound
res -all",

I have good shape in first initial structure and final frame, but there are
still clashed pbc shapes within several frame structures.

Could you let me know where I made a mistake?



Sangbae Lee
Research Fellow
Beckman Research Institute of The City of Hope
1500 Duarte Rd
Duarte, CA 91010
Cell> (352) 871-3073
Work> (626) 329-8111, x60618
E-mail> or

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