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 <jalem...@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
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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
jalem...@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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
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