[gmx-users] No group in index file?

[Justin Lemkul]

On 10/31/13 3:52 PM, Xu Dong Huang wrote:
> 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?
>

What version of Gromacs are you using?  With 4.6.3, I get sensible output.

-Justin

> 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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-- 
==================================================

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

==================================================