Ozge Engin skrev:
Hi all,
I am trying to translate the peptide within the simulation box. I have
a box with dimensions of 3.8 3.0 3.0 nm^3, and I want to put the
peptide on top of the box. In order to that I used the following
command line:
editconf -f pep.pdb -box 3.8 3.0 3.0 -translate 0 0 1.5 -o trans.pdb
The peptide is not translated, but sitting at the center of the box.
Why is the case? Any suggestions?
Thanks in advance
--
Ozge Engin
Because -c is implied by -box. excerpt form editconf -h output:
-[no]c bool no Center molecule in box (implied by -box and -d)
You'll have to do the -box and the -translate in two sequential passes
through editconf.
--
-----------------------------------------------
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
er...@xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys
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