[gmx-users] No group in index file?

[Xu Dong Huang]

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
> 
> ==================================================
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists