[gmx-users] g_chi again

[quantix1 at gmx.de]

Hi again,

I have edited the aminoacids.dat file and the simulations have run fine
(technically).
However, the i j k l  in chi.log do not correspond to atoms describing phi,
psi
and omega. Does anyone have an explanation for that. What could I have done
wrong?
Thanks,
Uwe

> quantix1 at gmx.de wrote:
> > Dear all,
> > 
> > I am trying to analyze backbone angles with g_chi. However, somehow the
> > angles are not
> > recognized properly by the program. I have introduced a couple of new
> > residue types.
> > Does this cause the problem?  I'm using the united atoms gromacs force
> > field.
> 
> In the Gromacs data dir ($GMXDATA/top IIRC), there is a file called
> aminoacids.dat which lists all residue names that are considered protein
> AA's. g_chi should print out a line where it says it is opening the file.
> You can copy it to your working directory, and append your residues.
> Possibly, the first line of the file contains the number of entries in
> the file and should be updated as well.
> 
> 
> -- 
> Groetjes,
> 
> Anton
>   _____________ _______________________________________________________
> |             |                                                       |
> |  _   _  ___,| K. Anton Feenstra                                     |
> | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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> | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
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