[gmx-users] Re:pdb2gmx - gromacs 3.2

David spoel at xray.bmc.uu.se
Tue Feb 17 08:17:01 CET 2004

On Tue, 2004-02-17 at 01:28, Wei Fu wrote:
> Hi, I have the same pdb2gmx problem when using Gromacs3.2. just copy
> FF.dat from previous version, it works.
> The other problem is that when I using "editconf -f $file.gro -o
> $file2.gro -d 1.0
> some atoms is out of box when using both gromacs3.1.4 and gromacs3.2
> version. 
> So, I try to using "editconf -f input.gro -princ -o output.gro -d 1.0"
> by gromcas3.2 to solve it, while
> I found the output.gro file is totally wrong, but when I use gromacs3.1.4
> do the same thing, it generates the correct coodinate. But it still
> has some atoms outside the box. The reason is that my protein has abnormal
> shape.
If it's a protein there is no such thing as abnormal...

> Should I use -c x y z to ajust box's position? Among them, x y z is a
> dummy point that is not the coordinate of atom. Any hit is appreciated.
with -center x y z you can center the protein in the box. If a part
sticks out it doesn't matter, as long as the protein does not "see" it's
own image.

The -c option is not functional right now...

> Linda 
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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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