[gmx-users] gromacs

Justin A. Lemkul jalemkul at vt.edu
Tue Oct 14 21:01:06 CEST 2008

He, Yang wrote:
> Hi all users,
> I juse encountered a problem when I run the code about the course grain for DNA,
> it shows like this
> creating statusfile for 1 node...
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
> checking input for internal consistency...
> calling cpp...
> In file included from ffyxh.itp:8,
>                  from hust.top:11:
> ffyxhnb.itp:25:61: warning: no newline at end of file
> In file included from ffyxh.itp:9,
>                  from hust.top:11:
> ffyxhbon.itp:26:5: warning: no newline at end of file
> In file included from hust.top:65:
> ffyxh.atp:6:34: warning: no newline at end of file
> hust.top:76:17: warning: no newline at end of file
> processing topology...
> Generated 32 of the 36 non-bonded parameter combinations
> -------------------------------------------------------
> Program grompp, VERSION 3.3.1
> Source code file: toputil.c, line: 61
> Fatal error:
> Atomtype 'OW' not found!
> I have tried to solve that , but it did not still work . So anyone of you can tell me how to solve that.

Well, what have you done to solve it?  From the messages grompp is printing out, 
it looks like the format of your files is badly mangled.  You're calling 
parameters for an atomtype which does not exist within the force field you've 
apparently created.  Parameters need to be defined within the .atp, *bon.itp, 
and *nb.itp files for it to be recognized.


> Thank you in advance.
> Yang
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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