[gmx-users] syntax for gmx distance

[Nash, Anthony]

Thanks Teemu,

I’ll look into this further.

Thanks
Anthony 



On 14/09/2015 12:32, "Teemu Murtola" <teemu.murtola at gmail.com> wrote:

>The error message really looks like that your shell does not understand
>the
>quoting. You need to pass the whole selection as a single command-line
>parameter (which your quotes in principle would do), but the error message
>indicates that each word is getting parsed as a separate selection, so
>your
>shell is passing them as separate arguments.
>
>Best regards,
>Teemu
>
>On Mon, Sep 14, 2015, 11:28 Nash, Anthony <a.nash at ucl.ac.uk> wrote:
>
>Dear all,
>
>I understand that this is quite a basic question, but I think I need a
>fresh set of eyes to figure out what¹s going on with gmx distance -select
>syntax.
>
>In my index file, I have 23 groups, two of which are ³ZINC² and ³CARBONYL²
>
>Based on numerous mail archive suggestions and the gromacs website change
>in tools page, I¹m using:
>
>$CHEM/rungromacs505 gmx distance -n index.ndx -f umb_1_all.trr -s
>umb_1_umb.tpr -oh umb_1_distance_hist.xvg -oall umb_1_distance.xvg -select
>'com of group "ZINC" plus com of group "CARBONYL"'
>
>Which kicks up the error:
>
>Invalid command-line options
>  In command-line option -select
>    In keyword 'com'
>      required parameter 'of' not specified
>    invalid selection 'com'
>  In command-line option -select
>    syntax error
>    invalid selection 'group'
>  In command-line option -select
>    syntax error
>    invalid selection 'plus'
>  In command-line option -select
>    In keyword 'com'
>      required parameter 'of' not specified
>    invalid selection 'com'
>  In command-line option -select
>    syntax error
>    invalid selection 'group'
>
>I¹d appreciate any suggestions. I¹ve also tried to do *something* via the
>interactive command line (when -select is not supplied), but what it¹s
>asking for is a bit cryptic.
>
>Thanks
>Anthony
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