[gmx-users] gmx ff all H again

David spoel at xray.bmc.uu.se
Thu Feb 24 06:40:44 CET 2005

On Wed, 2005-02-23 at 19:14 -0300, Alan Wilter Sousa da Silva wrote:
> Hi list!
> I was able to find out the origin of problems when running grompp 3.2.1 
> with ff=5 (gromos ff with all Hydrogens).
> I tested it with gmx version 3.1.4 and 3.2.1.
> It works fine with the first but not with the second (Fatal error: 
> Atomtype 'K' not found!)
> The reason is that the pdb2gmx 3.2.1 generate top file with line #include 
> "ions.itp" already included. If you comment with ";" this line, thus will 
> be able to run all the rest. I have to metion that the same would happen 
> if you insert such line in top file and run grompp 3.1.4.
> So, how could I insert ions now? I know that we will never run gmx with 
> such ff for sure, but...
> I tried to check ions.itp file and noted that is missing _FF_GROMACS2 
> definition. I did some changes but I failed in provindig you all a 
> final solution. Sorry.
> If someone could help here, I'd appreciate it very much.
> TIA and Cheers,

remove K from ions.itp

> Alan
> --------------------------
> Alan Wilter Sousa da Silva
> --------------------------
> Projeto BioPAUA - HP/LNCC
> Petrópolis (RJ), Brasil
> www.lncc.br/~alan
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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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