[gmx-users] Fatal error: Atomtype 'OS' not found!

[David]

On Wed, 2004-10-06 at 18:49, Yunfeng Hu wrote:
> In fact that is what I did. Here is what my topology file looks like:
> ;
> ;       File '7a1.top' was generated
> ;       By user: yunfenghu (501)
> ;       On host: Yunfeng-Hus-Computer.local
> ;       At date: Thu Sep 30 17:46:23 2004
> ;
> ;       This is your topology file
> ;       "Uh-oh .... Right Again" (Laurie Anderson)
> ;
> ; Include forcefield parameters
> #include "ffG43a1.itp"
> #include "cocaine.itp"

Most likely your file cocaine.tip also includes a forcefield statement
and/or atomtypes and/or charges in cocaine.itp have to be adapted to
ffG43a1 (which are different than ffgmx).

> 
> [ moleculetype ]
> ; Name            nrexcl
> Protein_L           3
> 
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass  
> typeB    chargeB      massB
>       1         NL      1    ASP      N      1      0.129    14.0067   ; 
> qtot 0.129
>       2          H      1    ASP     H1      1      0.248      1.008   ; 
> qtot 0.377
>       3          H      1    ASP     H2      1      0.248      1.008   ; 
> qtot 0.625
>       4          H      1    ASP     H3      1      0.248      1.008   ; 
> qtot 0.873
> ......
> [ system ]
> ; Name
> Protein in water
> 
> [ molecules ]
> ; Compound        #mols
> Protein_L           1
> COC                 1
> SOL              6502
> 
> On Oct 6, 2004, at 12:52 AM, Daan van Aalten wrote:
> 
> >
> > Hi
> >
> > You have to manually edit the complex.top to include the #include
> > statement as explained in detail in the Gromacs-ligand tutorial 
> > available
> > on the PRODRG FAQ page
> >
> > Daan
> >
> > On Tue, 5 Oct 2004, Yunfeng Hu wrote:
> >
> >> Hi, I used prodrg to obtain a topology file for the ligand and
> >> generated the complex topology file of a enzyme-ligand complex after
> >> modifying the enzyme topology file. After adding water box, grompp
> >> complains about atomtype OS not found which seems strange. I have 
> >> found
> >> a similar discussion in the mailing-list before and no final solution
> >> was offered. Here are the commands I used:
> >>
> >> pdb2gmx -merge -f complex.pdb -p complex.top -o complex.gro
> >> editconf -bt cubic -f complex.gro -o complex_h2o.gro -c -d 0.85
> >> genbox -cp complex_h2o.gro -cs spc216.gro -o complex_b4em.gro -p
> >> complex.top
> >> grompp -f em.mdp -c complex_b4em.gro -p complex.top -o complex_em.tpr
> >> ...
> >> creating statusfile for 1 node...
> >>
> >> checking input for internal consistency...
> >> calling /usr/bin/cpp...
> >> processing topology...
> >> Generated 279 of the 1225 non-bonded parameter combinations
> >> Cleaning up temporary file grompptjdQeY
> >> Fatal error: Atomtype 'OS' not found!
> >>
> >>
> >> Thank you for any suggestions.
> >>
> >> -Eric
> >>
> >> _______________________________________________
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> >>
> >
> >
> ###################################
> Yunfeng Hu, Ph.D
> Research Associate
> Department of Molecular Biology, MB-5
> The Scripps Research Institute
> 10550 North Torrey Pines Road
> La Jolla, CA 92037
> Tel. (858) 784-2204
> Fax. (858) 784-2860
> Emal: yunfeng at scripps.edu
> Web: http://www.scripps.edu/~yunfeng
> ###################################
> 
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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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