[gmx-users] FATAL ERROR

Marvin Seibert marvin at xray.bmc.uu.se
Fri Sep 23 09:53:26 CEST 2005

On Sep 23, 2005, at 8:30 AM, Amol D. Atre wrote:

> Hello all,
> While running pdb2gmx for cpeptide.pdb included in tutor/gmxdenmo  
> folder I
> am getting,
> FATAL ERROR: One of the box vectors is shorter than twice the cut-off
> length. Increase the box size or decrease rlist.

You probably already have a simulation box specified in the pdb file  
(several values on the last line of the file). Check that the file  
contains only lines that begin with ATOM or END).

> Can anybody throw some light on this?
> OS: Linux Fedora Core
> Command line: pdb2gmx -f cpeptide.pdb -o conf.gro -p topol.top -i  
> posre.itp
> Thanking in advance.
> Regards,
> Amol D. Atre.
> Lab No.A002,
> Chemical Engineering Department,
> Mumbai University Institute of Chemical Technology,
> Matunga(E), Mumbai-400019.
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