[gmx-users] still can not run md for creatine

[Mark Abraham]

On 15/11/2010 8:45 PM, Olga Ivchenko wrote:
> Dear All,
>
> I still have troubles of starting running md for creatine. For which I 
> created topology using PRODRG programm.
> The only difference between creatine.top and creating.itp is that 
> creatine top has additional lines:
>  #include "ffgmx.itp"
> #include "creatine.itp"

That won't work because you effectively have the same contents twice. 
See http://www.gromacs.org/Documentation/Include_File_Mechanism

>
> Also please can you tell me where can I get "ffgmx.itp" file?

You probably don't want to. ffgmx has been deprecated for most of a 
decade. Use the PRODRG 2.5 beta server that will generate a 
GROMACS-compatible topology file. Other suggestions for other force 
fields may be found in step 5 of 
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation?highlight=Swissparam. 
You should choose the forcefield based on what you want to observe, 
rather than by what is available for the first tool that comes to hand.


> By trying to run md I am getting an error: Fatal error:
> moleculetype UNK is redefined

Yep, you have the same contents twice. Hence "redefined"

Mark