[gmx-users] phi / psi values using g_chi

[XAvier Periole]

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, 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.
>
> 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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