[gmx-users] Error with "grompp"

Elie M elie.moujaes at hotmail.co.uk
Fri Oct 5 19:00:13 CEST 2012

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?


> Date: Thu, 4 Oct 2012 21:25:29 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Error with "grompp"
> On 10/4/12 5:56 PM, Elie M wrote:
> >
> > I guess the first parameter of each pair is easy to find. what about kb? k theta?..... kb is the force constant isnt it? any reference about a method how to calculate them please? pr anything atht might be of help.
> >
> Bonded parameters are generally based on vibrational spectra and X-ray data. 
> For OPLS, the bonded parameters were originally taken from an AMBER parameter 
> set in the mid-1980's and have some terms have subsequently been revised over time.
> -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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