[gmx-users] phi / psi values using g_chi
x.periole at rug.nl
Wed Mar 11 18:06:34 CET 2009
Thanks for the link.
I then do not understand what is happening because I get the same
with g_chi and g_rama! Are you sure you were using the gmx-3.3.1? And
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
Anyone would have changed the code and forgot to update the comment on
choice of the atoms to calculate the phi/psi angles in g_chi ?
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, chris.neale at utoronto.ca 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.
> 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
> This adds noise to your date. Use g_rama instread.
>> 2) Which Karplus equation parameterization is used to calculated
>> the Jcouplings?
> no comment here.
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