[gmx-users] wrong bonded information in .top/.rtp file produced by g_x2top

zhhxu zhhxu at home.ipe.ac.cn
Thu Feb 28 08:45:28 CET 2013

hi all :

I prepared  top and rtp file for graphite using a command:

        g_x2top -f input.gro -r output -o  output in GMX (V 4.5.5).

       A  obvious mistake itp file is posted as below:
[ bonds ]  
     C1  C3776   1.420e-01   4.000e+05  
     C5  C3780   1.420e-01   4.000e+05
for example,the distance between  C1 and C3776 is at least 10 nm.
 the coordination is below:
1GRA       C1    1   0.000   0.000   0.000
1GRA    C3776 3776   0.000  10.068   0.000 

Thanks in advance for any suggestion.


     zhhxu  PhD student

  Institute of Process Engineering, Chinese Academy of Sciences

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