[gmx-users] gmx ff all H again

Alan Wilter Sousa da Silva alan at lncc.br
Wed Feb 23 23:14:22 CET 2005

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,

Alan Wilter Sousa da Silva
Projeto BioPAUA - HP/LNCC
Petrópolis (RJ), Brasil

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