[gmx-users] g_select error

[Justin Lemkul]

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;
close;

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

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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