[gmx-users] Re: error in grompp command

Justin A. Lemkul jalemkul at vt.edu
Mon Nov 29 15:05:46 CET 2010

Please keep all Gromacs-related correspondence on the gmx-users list.  I am not 
a private help service.  I am CC'ing the list and would ask that all further 
discussion occur there.

rasmiprava samal wrote:


> ERROR 1 [file topol.top, line 20758]:
>   No default Ryckaert-Bell. types

You have a dihedral that does not exist in the force field.  Either find 
parameters for it, or derive them yourself.

> Opening library file /usr/share/gromacs/top/spc.itp
> Opening library file /usr/share/gromacs/top/ions.itp
> Excluding 3 bonded neighbours molecule type 'Protein_A'
> Excluding 2 bonded neighbours molecule type 'SOL'
> NOTE 1 [file topol.top, line 27729]:
>   System has non-zero total charge: -3.640000e+00

Your topology is badly broken.  This net charge should be an integer.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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