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

Daan van Aalten vdava at davapc1.bioch.dundee.ac.uk
Wed Oct 6 09:52:01 CEST 2004


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


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
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list