[gmx-users] Error with "grompp"

Justin Lemkul jalemkul at vt.edu
Sat Oct 6 19:26:38 CEST 2012

On 10/6/12 1:18 PM, Elie M wrote:
> This is what I did. For example one of the [bonds] problems is a bond between S and one of the carbons C in the thiophene molecule. In the n2t file. I have added OPLSA_734 S because it si related to " all-atom S: thiophenol (HS is #204)"; the corresponding C was assigned an OPLSA_735 I have looked for the symbols for these two: the first is SH and the other is CA so in [bondtypes] in ffoplsaabon.itp I have added a line:
> SH    CA      1    0.15925   186649.5   ;
> However the error related to this bond is still present. I was just thinking mabye that OPLSAA_734 for S is sulfur connected to Hydrogen  because the symbol is SH?? maybe this is the source of the error and I have to redefine things in the .n2t file?

It may be a matter of the order of the atoms.  SH is indeed sulfur (you can tell 
by the mass in atomtypes.atp and the fact that the first letter is S).  The 
corresponding H atom is HS, so that's not the problem.  The parameters for this 
bond are already in ffbonded.itp (ffoplsaabon.itp in your case, with a pre-4.5 

   CA    SH      1    0.17400   209200.0   ; wlj



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


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