[gmx-users] Atomtype 'C' not found!

[David van der Spoel]

On Tue, 2004-03-30 at 15:30, Raghunadha Reddy Burri wrote:
> Dear David,
> Please check my problem, I am using GMX 3.1.4
> Thanx in advance
> Bye
> RB
probably the urea topology does not fit the forcefield. it will only
work with ffgmx i think.
> 
> 
> 
> On Monday 29 March 2004 10:59, Raghunadha Reddy Burri wrote:
> > Dear GMX users,
> >
> > While I am using my peptide in Urea+h2o, I got fatal error please help me
> > to overcome this error.
> >
> > > grompp -f em.mdp -c dpep_b4em.gro -p dpep.top -o dpep_em.tpr
> >
> > .
> > .
> > .
> >
> > Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
> > checking input for internal consistency...
> > calling /lib/cpp...
> > processing topology...
> > Generated 241860 of the 241860 non-bonded parameter combinations
> > Generating 1-4 interactions: fudge = 0.5
> > Generated 241860 of the 241860 1-4 parameter combinations
> > Cleaning up temporary file gromppgkQJ7e
> > Fatal error: Atomtype 'C' not found!
> >
> >
> >
> >
> >
> > My topology file last few lines (dpep.top )
> >
> >
> > ; Include Position restraint file
> > #ifdef POSRES
> > #include "posre.itp"
> > #endif
> >
> > ; Include water topology
> > #include "urea.itp"
> > #include "spc.itp"
> >
> > #ifdef POSRES_WATER
> > ; Position restraint for each water oxygen
> > [ position_restraints ]
> > ;  i funct       fcx        fcy        fcz
> >    1    1       1000       1000       1000
> > #endif
> >
> > [ system ]
> > ; Name
> > DPEP in water
> >
> > [ molecules ]
> > ; Compound        #mols
> > Protein             1
> > Urea		    1
> > SOL              2985
> >
> >
> > Thanx for your time and consideration, any help will be really appreciated.
> >
> > RB
> >
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. 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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