[gmx-users] Re:pdb2gmx - gromacs 3.2

[Wei Fu]

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.
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.

Linda