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

David spoel at xray.bmc.uu.se
Tue Oct 5 21:33:31 CEST 2004

On Tue, 2004-10-05 at 19:48, 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!
you probably lost a force field inclusion and/or mix two force fields.
> Thank you for any suggestions.
> -Eric
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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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