[gmx-users] g_select error

[Justin Lemkul]

On 11/26/12 2:08 PM, Albert wrote:
>
> hello:
>
>   I am going to calculate the number of water molecules within 6 A of
> residue 114 by following command:
>
>
> g_select -f md.xtc -s npt3.pdb -os size.xvg -select "resid 114 and rdist
> < 0.6"
>
>
> but it said:
>
>
> 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 'resid 114 and rdist < 0.6'
>
> -------------------------------------------------------
> 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
> -------------------------------------------------------
>

You haven't defined rdist to actually be anything.  If you need to be using 
multi-line selections, you should be providing a selection.dat file to -sf 
instead of using single-line statements to -select.

Something like g_select -select 'resname SOL and name OW within 0.6 of resid 
114' should do the trick, but I haven't actually tried that so I'm not 100% sure.

-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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