[gmx-users] No group in index file?

[Riccardo Concu]

Dear Xu,
you have to use the make_ndx option if I'm not wrong.
The syntax should be make_ndx -f xxx.gro -o index.ndx
Cheers,

-----Original Message----- 
From: Xu Dong Huang
Sent: Thursday, October 31, 2013 8:52 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] No group in index file?

Dear all,

so after I opened angle.ndx file in a text editor, the file appears to be 
blank. How can I properly make a index file since the command I issued seems 
to produce a blank index file? Is there something wrong with my input 
regarding npt.tpr?

Thanks for your input,

Xu Huang

On Oct 31, 2013, at 1:38 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/31/13 1:36 PM, Xu Dong Huang wrote:
>> Dear all.
>>
>> Since I am interested in finding the average angle, dihedrals in my 
>> system, I attempted to use g_angle, but then I realized I need to make 
>> index file using mk_angndx,
>>
>> I issued the following:
>> mk_angndx -s npt.tpr -n angle.ndx
>>
>> and then i used g_angle -f not.xtc -n angle.ndx -ov 
>> angle.xvg -noperiodic -type angle
>>
>> and then I get the following error:
>> Fatal error:
>> Error: no groups in indexfile
>>
>> How can my index file not have the groups in there? How can I go about 
>> fixing this
>>
>
> Inspect it with a text editor and/or gmxcheck.
>
> -Justin
>
> -- 
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
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