[gmx-users] US perl scripts fails index error

[Yoo Chan Myung]

I had same problems even I have nothing wrong in running gmx distance.
Weirdly, after I excise * &>/dev/null *in distance.pl I could finally get
summary_distance.dat without any blanks.

such as..
system("gmx distance -s ../pull.tpr -f conf${i}.gro -n ../index.ndx -oall
dist${i}.xvg -select \'com of group \"DPPC\" plus com of group \"ARG\"\'");


On Tue, Jan 5, 2016 at 9:36 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/5/16 4:06 AM, Nikhil wrote:
>
>> Thank you very much Justin,
>> i fixed it,i run the script when i analyzing the summary_distance.dat i
>> seen
>> some filed is left blank,as below
>> 389     3.989
>> 390     4.029
>> 391     4.014
>> 392
>> 393     4.103
>> 394     4.147
>> 395
>> 396     4.188
>> 397
>> 398
>> 399     4.157
>> 400     4.188
>> 401     4.324
>> 402     4.236
>> 403     4.239
>> 404
>> 405
>> 406     4.275
>> 407
>> 408     4.386
>> 409     4.359
>> 410     4.391
>>
>> 392,395,397,398 so on ,is there anything wrong in system?
>>
>>
>>
> You shouldn't get blank values.  That means something failed in the gmx
> distance execution.  Run the command on one of the failed configurations
> and see what the error is.  Just relying on a compiled output file provides
> you with nothing useful in terms of diagnostics.
>
> -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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