[gmx-users] g_chi again
spoel at xray.bmc.uu.se
Fri May 2 13:20:01 CEST 2003
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
> However, the i j k l in chi.log do not correspond to atoms describing phi,
> and omega. Does anyone have an explanation for that. What could I have done
isn't it atom numbers -1 ?
> > 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/ |
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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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