[gmx-users] grompp problem

[David]

On Thu, 2003-10-16 at 07:35, Vivek Raut wrote:
> 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
> 
probably some weird residues in your topology 
check at line 1371 which atoms are listed there and find out why these
aren't in the force field files.

> what should I do now??
> 
> I have been running similar simulations but it never gave me this error, 
> why is it giving one now??
> 
> Vivek
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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