[gmx-users] gmx chi output clarification

Justin Lemkul jalemkul at vt.edu
Wed Feb 17 13:50:04 CET 2016

On 2/17/16 7:11 AM, Francesco Carbone wrote:
> Thank you Justin,
> I'm not a pro in C, but I think that in the code, the omega angle is
> defined as CA-C-N-CA (Bug #953 discussed this)
> ...
> dl[i].j0[edOmega] = n/4;
> id[n++] = dl[i].atm.minCalpha;
> id[n++] = dl[i].atm.minCalpha;
> id[n++] = dl[i].atm.N;
> id[n++] = dl[i].atm.Cn[1];
> ...
> I then calculated the same angle using gmx chi (5.0.4) , g_chi (4.6), gmx
> angle (5.0.4) and pdbtorsion (an in house tool that is always right ,of
> course this is what my supervisor says :D)
> If I use pdbs dumped from a trajectory, all of them provides similar values
> (3-4-0.2-1).
> On the other hand, if I'm using a pdb coming from outside source (rcsb.org),
> gmx chi is the only one that gives "flipped" values.
> If I remove the flip (173 -180° ) I obtain a plausible value, but then why
> don't I see this "flip" when I use "gmx chi" with a trajectory or a pdb
> dumped from the trajectory?

Hopefully whoever wrote the code (David?) will comment, as this is the extent of 
what I know about gmx chi (since I haven't used it in a long time).



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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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