Bug #1481
g_chi output file chi.log reports atomic definitions for phi and psi that do not correspond to the angles output in the .xvg files
Description
g_chi -h reports:
* phi and psi dihedrals are calculated in a non-standard way, using H-N-CA-C for phi instead of C(-)-N-CA-C, and N-CA-C-O for psi instead of N-CA-C-N(+). This causes (usually small) discrepancies with the output of other tools like g_rama.
The file chi.log then lists the atoms used to evaluate the dihedral angles:
Residue VAL2 Angle [ AI, AJ, AK, AL] #tr/ns S^2D -------------------------------------------- Phi [ 19, 18, 20, 32] 0.00 1.00 Psi [ 18, 20, 32, 33] 0.00 1.00 Chi1[ 18, 20, 22, 24] 0.00 1.00
And, consistently, the phi dihedral (19,18,20,32 from above) is H-N-CA-C :
-bash-4.1$ head -40 restr.gro Green Red Orange Magenta Azure Cyan Skyblue in water 54303 1GLU N 1 3.250 1.491 2.817 1GLU H1 2 3.327 1.535 2.864 1GLU H2 3 3.273 1.395 2.792 1GLU H3 4 3.231 1.539 2.731 1GLU CA 5 3.128 1.494 2.900 1GLU HA 6 3.099 1.598 2.916 1GLU CB 7 3.012 1.432 2.819 1GLU HB1 8 2.999 1.328 2.848 1GLU HB2 9 3.039 1.434 2.712 1GLU CG 10 2.884 1.512 2.837 1GLU HG1 11 2.907 1.618 2.820 1GLU HG2 12 2.848 1.500 2.938 1GLU CD 13 2.777 1.466 2.737 1GLU OE1 14 2.709 1.556 2.684 1GLU OE2 15 2.773 1.345 2.711 1GLU C 16 3.141 1.430 3.039 1GLU O 17 3.053 1.450 3.121 2VAL N 18 3.253 1.362 3.073 2VAL H 19 3.318 1.335 3.000 2VAL CA 20 3.276 1.304 3.207 2VAL HA 21 3.181 1.292 3.258 2VAL CB 22 3.338 1.164 3.193 2VAL HB 23 3.416 1.167 3.117 2VAL CG1 24 3.402 1.111 3.322 2VAL HG11 25 3.435 1.008 3.308 2VAL HG12 26 3.489 1.170 3.349 2VAL HG13 27 3.329 1.114 3.404 2VAL CG2 28 3.229 1.065 3.149 2VAL HG21 29 3.272 0.966 3.133 2VAL HG22 30 3.151 1.058 3.225 2VAL HG23 31 3.184 1.098 3.056 2VAL C 32 3.359 1.396 3.297 2VAL O 33 3.318 1.422 3.410 3TRP N 34 3.471 1.452 3.248 3TRP H 35 3.508 1.420 3.160 3TRP CA 36 3.549 1.552 3.324 3TRP HA 37 3.579 1.510 3.421 3TRP CB 38 3.676 1.589 3.246
However, looking at the value returned from g_chi in the .xvg file, it is clear that g_chi is either (a) actually using C(i-1)-N-CA-C for phi, or (b) somehow using the computed H-N-CA-C dihedral angle to estimate the C(i-1)-N-CA-C dihedral angle.
This lead me to scripting problems when I tried to extract dihedral angle definitions and reference angles for use in dihedral restraints because the reported angle does not match the reported atomic definition.
Complicating things even more, bug 53 suggests that g_chi and g_rama are now exactly the same for phi and psi (except the terminal residues). See also https://www.mail-archive.com/gmx-users@gromacs.org/msg19991.html and my new calculations indicate that g_rama and g_chi give the same backbone dihedrals.
Therefore, I suggest that:
(a) the warning about non-standard torsions be changed to indicate that this only relates to terminal residues
(b) the definition of atoms printed in chi.log be corrected.
Related issues
History
#1 Updated by David van der Spoel over 6 years ago
Related to #1235
#2 Updated by David van der Spoel over 6 years ago
We are using the hydrogen to define the Phi angle. Since we might not want to change this in de bug fix release I would prefer to change the help text.
#3 Updated by Rossen Apostolov over 6 years ago
- Related to Bug #1235: peptide dihedral angle definitions violate IUPAC added