[gmx-users] Error with "grompp"

[Justin Lemkul]

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

-- 
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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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