[gmx-users] g_chi again

[David]

On Fri, 2003-05-02 at 12:16, quantix1 at gmx.de wrote:
> 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?
isn't it atom numbers -1 ?
> 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 |
> > |(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
> > | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
> > |             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
> > |             | "If You See Me Getting High, Knock Me Down"           |
> > |             | (Red Hot Chili Peppers)                               |
> > |_____________|_______________________________________________________|
> > 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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