[gmx-users] No group in index file?
ric.concu at gmail.com
Thu Oct 31 20:59:47 CET 2013
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
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?
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
Thanks for your input,
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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