[gmx-users] gmx chi output clarification

Francesco Carbone fra.carbone8 at gmail.com
Tue Feb 16 16:16:50 CET 2016

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
gmx chi -s 2bhl_fixed.pdb -f file.xtc -o output.xvg -g logfile.log -omega

I obtain values close to 180°,suggesting that  the Proline is in trans.

How is it possible?

I also tried to set -ramomega, but I don't see any xpm file being created.

Am I doing something wrong?



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