[gmx-users] Error with "grompp"

Justin Lemkul jalemkul at vt.edu
Thu Oct 4 22:25:35 CEST 2012

On 10/4/12 4:22 PM, Elie M wrote:
> I guess now I get what is happening finally. Correct me if I am wrong.  The
> .top file was produced using an .n2t file (mine was ffoplsaamod.n2t) which
> was also modified to include atoms that were not there *but present in
> atomtypes.atp). The .top file describes all the bonds and angles in the
> molecule. This was successful. However the characteristics of some of those
> bonds are not described in the foplssabon.itp file; for example I have Sulfur
> in my molecule connected to carbon which has no entry in foplsaabon.itp and
> must be added to that file manually. I guess now I am in a position to check
> those bonds and add the relevant information which i will gather maybe from
> HYPERCHEM or ARGUSLAB??....A final question is in order here: what do the

You will have to calculate reasonable values in some way, yes.

> parameters (b0, kb), (th0, cth), (q0,cq), and (phi0, cp,mult) represent and
> in what units?

All of this is in the manual.



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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