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
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