[gmx-users] Error with "grompp"

Elie M elie.moujaes at hotmail.co.uk
Sat Oct 6 19:18:49 CEST 2012

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?


> Date: Fri, 5 Oct 2012 13:06:34 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Error with "grompp"
> On 10/5/12 1:00 PM, Elie M wrote:
> >
> > I was able to find reasonable values of kb and b0 and inserted the info into foplsaabon.itp. I am still getting an error; what I did is the following:
> > 1- I went to ffoplsaa.n2t to check the OPLSA_XXX of the atoms.2- Next I check the section [atomtypes] in fftoplsaa.nb and see to what symbol the oplsa_xxx corresponds for example (OW). If the problem was in the [bonds] directive, I plug the info there with the corresponding values of bo and kb and according to the format there, and I save.
> > 3- i run grompp again but in vain as I still get the same number of errors (as I expect they should decrease in number if things were fixed).
> > Am I still missing something that i should have done apart from filling in the numbers in ffoplsaabon.itp?
> >
> Whatever changes you made were apparently ineffectual.  You need to make sure 
> that you are adding parameters in the correct directives (i.e. bonds in 
> [bondtypes], angles in [angletypes], etc).  Without seeing exactly what you've 
> done, all I can say is that whatever you did wasn't correct.  The approach is 
> theoretically sound, though.
> -Justin
> -- 
> ========================================
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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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