Morteza Khabiri wrote:
Dear Mark,
Thanks for your help. As you said I define cpp path for my system. Now I
get 1 warning and the following error. To be mor clear, I also paste my
mdp file.
OK, but it's the .top file that is pertinent now.
checking input for internal consistency...
WARNING 1 [file md_bfgs.mdp, line unknown]:
Removing the rotation around the center of mass in a periodic system
(this is not a problem when you have only one molecule).
calling /lib/cpp...
processing topology...
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
Cleaning up temporary file gromppDFgrVF
-------------------------------------------------------
Program grompp, VERSION 3.3.3
Source code file: topio.c, line: 389
Fatal error:
Invalid order for directive defaults, file
""/usr/local/gromacs/share/top/ffoplsaa.itp"", line 18
You're mangling your .top file, either with a misordered or extra
#include to your forcefield file.
Mark
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