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 <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
--
==================================================
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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