[gmx-users] tfe.itp

Justin A. Lemkul jalemkul at vt.edu
Wed Aug 20 11:53:24 CEST 2008

shahrbanoo karbalaee wrote:
> Dear justin
> I made topology top for tfe with gromos53a5.and I solvated in spc and
> 40molecule tfe.I includeed tfe.itp in topology.but when I do grompp I
> get  this error.(I edit the name of atoms with name in rtp file HT)
> Generated 165 of the 1596 non-bonded parameter combinations
> ERROR 0 [file "topol.top", line 57]:
>   No default Proper Dih. types
> Cleaning up temporary file gromppsYSJRG
> -------------------------------------------------------
> Program grompp, VERSION 3.3.2
> Source code file: toputil.c, line: 61
> Fatal error:
> Atomtype 'HO' not found!
> -------------------------------------------------------
> my topology file is attached.

In the topol.top you've provided, you define all the necessary components for 
TFE, but then later call tfe.itp.  Why?  You've obviously got an inconsistency 

Think of it this way - in a topol.top for a protein generated by pdb2gmx, you 
don't generate all the protein parameters, then later on, call protein.itp 
within topol.top!  If you just have a system of TFE + water, then you can define 
the TFE parameters at the beginning of the .top, then just call spc.itp later.

I'm betting that within tfe.itp lies the problem.  Remove the call for tfe.itp 
and see how it goes, because you've already defined everything you need.


> best
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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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