[gmx-users] Re: error in grompp command

[Justin A. Lemkul]

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:

<snip>

> 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

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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