[gmx-users] Problem with g_chi options

Justin Lemkul jalemkul at vt.edu
Wed Jul 9 19:25:46 CEST 2014

On 7/9/14, 5:51 AM, Anna Stopka wrote:
> Hi everybody,
> I wrote last week, but nobody answered. So I write again, still having the same
> problem:
> I want do an analysis of my simulation with the tool g_chi.
> The problem is, that the optional output options don't work.
> I use the following command:
> g_chi -s config.gro -f traj.xtc -oh -all
> and all I get are the standard output files chi.log and order.xvg.
> I am not sure if it has something to do with the following warning I get:
> WARNING: not all dihedrals found in topology (only 1056 out of 1746)!
> Honestly, I don't understand why I get this warning, because all the
> input files are fine.

Have you tried using a .tpr file instead of a .gro file as the structure passed 
to -s?  I don't know how there can be any interpretation of a topology, given 
the fact that you haven't passed any topological information to g_chi.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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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