[gmx-users] No group in index file?
jalemkul at vt.edu
Thu Oct 31 21:16:14 CET 2013
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.
> 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 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.
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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