[gmx-users] syntax for gmx distance

[Nash, Anthony]

Thanks Teemu,

That was spot on. I simply took the -select argument and dropped it into a
text file then used the -sf option instead. Works perfectly.

Thanks again
Anthony 




On 14/09/2015 12:34, "Nash, Anthony" <a.nash at ucl.ac.uk> wrote:

>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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