[gmx-users] grompp problem

Vivek Raut vraut at CLEMSON.EDU
Thu Oct 16 07:36:01 CEST 2003

I am trying to run a simulation. I started with this sequence of commands: 
pdb2gmx, editcconf (to generate box), genbox ( to fill it with water), 
make_ndx, grompp...

Then I ran the following grompp command:

grompp -f em.mdp -po emout.mdp -c input.gro -n input.ndx -p input.top -pp 
output.top -o output.tpr

but it gives me this error:

WARNING 1 [file "1.top", line 1371]:
   No default Bond types, using zeroes

what should I do now??

I have been running similar simulations but it never gave me this error, 
why is it giving one now??


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