[gmx-users] g_select error

Justin Lemkul jalemkul at vt.edu
Thu Jan 10 12:25:48 CET 2013

On 1/10/13 4:08 AM, Albert wrote:
> hello:
>   I am trying to use g_select to make an index file with command:
> g_select_mpi -f md.xtc -s npt3.pdb -on density.ndx
> but it failed with messages:
> WARNING: Masses and atomic (Van der Waals) radii will be guessed
>           based on residue and atom names, since they could not be
>           definitively assigned from the information in your input
>           files. These guessed numbers might deviate from the mass
>           and radius of the atom type. Please check the output
>           files if necessary.
> Assertion failed for "g" in file
> /home/albert/Desktop/gromacs-4.6-beta3/src/gmxlib/sel
> dump core ? (y/n)

Apparently whatever you're tying to select requires a .tpr file as input to work 
rather than a .pdb file.



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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