I was under the impression that -box and -d should center the protein in the solvent box. It says in the manual- Center molecule in box (implied by -box and -d)<br>Jaya<br><br><br><div class="gmail_quote">On Mon, Sep 14, 2009 at 2:12 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5">jayalakshmi sridhar wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear GROMACS Users,<br>
I am new to GROMACS. I am trying to solvate my protein in a octahedral box.<br>
I used the following commands after generating the initial .gro and .top<br>
files.<br>
$ editconf -f 1z10_groinit.gro -o 1z10_groinit.gro -box 8.5 -d 0.85 -bt<br>
octahedron<br>
and then<br>
$ genbox -cp 1z10_groinit.gro -cs -o 1z10_groinit_b4em.gro -p<br>
1z10_groinit.top<br>
<br>
But when I visualize the solvated protein in VMD, I see that the protein is<br>
not centered in the box. All help is greatly appreciated. Thanks.<br>
Jaya.<br>
</blockquote>
<br></div></div>
Well you didn't tell it to center on the protein, so the result should be no particular surprise. Read editconf -h and genbox -h and see what you learn about how to center things. :-)<br>
<br>
Mark<br>
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</blockquote></div><br>