[gmx-users] missing parameters

[David van der Spoel]

On Fri, 2004-06-11 at 11:59, herbst at fhi-berlin.mpg.de wrote:
> But when I start a simulation with the molecule, it flies apart because
> there are no parameters! It only works when I add the parameters by hand
> to the topology file! Somehow the parameters from the .itp files are not
> used. Do you have an idea what I shoudl do?

do you mean that there are no parameters for the standard residues, or
for your new residue?
In the latter case you need to add them to the rtp file
> 
> 
> > On Fri, 2004-06-11 at 11:18, herbst at fhi-berlin.mpg.de wrote:
> >> Hello,
> >>
> >> I created a topology file for a protein using the gromacs forcefield.
> >> The
> >> topology was ok but in the lists of bonds, angles etc. there are no
> >> parameters.  Only the parameters for a residue which I had entered to
> >> the
> >> .rtp file myself appeared. What did I do wrong ?
> > most parameters are in library files.
> > ffXXXnb.itp ffXXXbon.itp.
> >
> > grompp will tell you when parameters are missing.
> >> All other residues are standard amino acids.
> >>
> >> Thanks,
> >> Anna
> >> _______________________________________________
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> > --
> > David.
> > ________________________________________________________________________
> > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > 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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> >
> 
> _______________________________________________
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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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