[gmx-users] syntax for gmx distance

[Justin Lemkul]

On 9/14/15 4:28 AM, Nash, Anthony 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.
>

What is $CHEM/rungromacs505?  I suspect that's your problem.

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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