[gmx-users] gmx chi output clarification

Justin Lemkul jalemkul at vt.edu
Tue Feb 16 17:10:18 CET 2016

On 2/16/16 10:16 AM, Francesco Carbone wrote:
> good afternoon,
> I'm trying to study the values of the omega dihedral (peptide bond) for a
> specific Proline in my protein.
> This Proline is known to exists in both cis and trans conformation(cis
> while binding).
> In the pdb I used as starting point for the simulation (2bhl.pdb) the
> Proline (172) is in cis configuration.
> This is confirmed both by the people who make the pdb and also by vmd ("fix
> cis peptide bond" tool) .
> If I run the command:
> gmx chi -s simulation.tpr -f simulation.xtc -o output.xvg -g logfile.log
> -omega -all
> I can see that the Proline has values in the neighbourhood of 0° ( +-20° ),
> which is fine, being in cis.
> The problem is that if I try to calculate the same dihedral in the original
> structure (2bhl.pdb), using:
> gmx chi -s 2bhl_fixed.pdb -f 2bhl_fixed.pdb -o output.xvg -g logfile.log
> -omega -all
> or
> gmx chi -s 2bhl_fixed.pdb -f file.xtc -o output.xvg -g logfile.log -omega
> -all
> I obtain values close to 180°,suggesting that  the Proline is in trans.
> How is it possible?

IIRC gmx chi does not use H atoms in the calculations of these dihedrals. 
Confirm with gmx angle -type dihedral that everything checks out.


> I also tried to set -ramomega, but I don't see any xpm file being created.
> Am I doing something wrong?
> Regards,
> Francesco


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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