Hi Chris,
Thanks for the link.
I then do not understand what is happening because I get the same
exact values
with g_chi and g_rama! Are you sure you were using the gmx-3.3.1? And
not an
earlier version?
Note that in the code of gmx-3.1.4 and gmx-3.2.1 the non-standard
definition is used
but in the gmx-3.3.1 the code is changed and the standard definition
is used.
Anyone would have changed the code and forgot to update the comment on
the
choice of the atoms to calculate the phi/psi angles in g_chi ?
XAvier.
---------------------
Data:
g_chi / from the phi-psi files for Ala15
10000 -112.924 42.8174
10100 -114.15 57.1768
10200 -82.0442 -11.6453
10300 -99.8691 36.5998
10400 -83.1319 -20.2397
g_rama / extracting the Ala15 data
10000 -112.924 42.8174 ALA-15
10100 -114.15 57.1768 ALA-15
10200 -82.0442 -11.6453 ALA-15
10300 -99.8691 36.5998 ALA-15
10400 -83.1319 -20.2397 ALA-15
10500 -104.275 12.6959 ALA-15
On Mar 11, 2009, at 4:53 PM, [email protected] wrote:
two questions relative to g_chi from the gmx-3.3.1 but gmx-4.0.2
uses similar code.
1) In the header of g_chi obtained using the -h option there is a
"bug" that indicates that
the phi/psi angles are not calculated as the usual C(-)-N-CA-C and N-
CA-C-N(+) definitions
but H-N-CA-C and N-CA-C-O instead, respectively.
From both the code and the comparison of the values extracted with
g_chi and VMD, it
seems that the actual correct definition is used.
From what I can recall of 3.3.1, the incorrect definitions are used
and then there is a +180 that corrects for the strange definition.
Standard:
phi: C[i-1]-N-Ca-C
psi: N-Ca-C-N[i+1]
GROMACS g_chi:
phi: H-N-Ca-C minus 180deg
psi: N-Ca-C-O minus 180deg
(http://www.gromacs.org/pipermail/gmx-users/2007-February/025927.html)
This adds noise to your date. Use g_rama instread.
2) Which Karplus equation parameterization is used to calculated
the Jcouplings?
no comment here.
Chris.
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