[gmx-users] g_select error

Justin Lemkul jalemkul at vt.edu
Tue Nov 27 15:33:26 CET 2012

On 11/27/12 9:18 AM, Albert wrote:
> hello Justin:
>    thanks for kind tips.
>    I've tried both methods:
> g_select -f md.xtc -s npt3.pdb -os size.xvg -sf selection.dat
> g_select -f md.xtc -s npt3.pdb -os size.xvg -select 'resname SOL and name OW
> within 0.6 of resid 114'
> but they all failed with messages:
> --------------------log--------------------
> WARNING: masses and atomic (Van der Waals) radii will be determined
>           based on residue and atom names. These numbers can deviate
>           from the correct mass and radius of the atom type.
> selection parser: syntax error
> selection parser: invalid selection 'resname SOL and name OW within 0.6 of resid
> 114'
> -------------------------------------------------------
> Program g_select, VERSION 4.5.5
> Source code file: trajana.c, line: 1310
> Input error or input inconsistency:
> selection(s) could not be parsed
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------

Well, like I warned, I wasn't 100% sure of the syntax, so it was no guarantee 
that I was right.  Reading into the documentation and examples a bit, it seems 
that "resname SOL and name OW" should be enclosed within double quotes, within 
the single-quoted string.  Otherwise, use this selection.dat file:

waterO = name OW;
close = waterO and within 0.6 of resid 114;

It should be possible to do it in one line, but the above set of selections 
seems to work fine.



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


More information about the gromacs.org_gmx-users mailing list