[gmx-users] Error with "grompp"

Justin Lemkul jalemkul at vt.edu
Fri Oct 5 19:06:34 CEST 2012

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


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