[gmx-users] error in editconf

Justin Lemkul jalemkul at vt.edu
Tue Feb 19 14:00:42 CET 2013

On 2/19/13 4:53 AM, az kalsom wrote:
> hi all,
> i generated the ligand topology file by prodrg server and then i generated
> the .out file from gaussain software aund used itp adjuster to adjsut the
> charges in ligand itp file
> but still i am getting the bad box error when i run the editconf command
> why is this so what should i do to correct this ?

"Bad box" errors usually mean you don't have box vectors in the coordinate file 
or that the number of atoms specified in the .gro file is incorrect, leading to 
editconf reading a coordinate entry as box vectors.  Without the first 2 lines 
and last line of the .gro file, as well as the output of wc -l on the file, it's 
impossible to say what the real problem is.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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