[gmx-users] grompp error - incorrect number of parameters

[Justin A. Lemkul]

On 5/17/12 9:47 AM, Lara Bunte wrote:
> Hello
>
>
> After
>
>
> grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
>
>
> I got the error:
>
> Incorrect number of parameters - found 2, expected 4 or 4 for U-B.
>
>
> I thought that this could be an inconsistency be declaring the functions, but in my topology I have function 4 (for improper dihedrals):
>
>
> Out of topol.top
>
> [ dihedrals ]
> ;  ai    aj    ak    al funct            c0            c1            c2            c3
>      1     8     6     4     4    180   100
>
>
> And in my .rtp file in the CHARMM27 force field folder I have:
>
> Out of .rtp file
> ; bonds  angles  dihedrals  impropers
>       1       5          4        4
>
>
> and in my ffbonded.itp file I have:
> [ dihedraltypes ]
> ; i     j       k       l       func    q0      cq
> ON1     NN3A      CN1A       NN2U   4   180   100
>
>
> So in alle three files, ffbonded.itp, topol.top and the .rtp parametrization file I have the function 4 for the improper dihedrals.
>
>
> What is the problem?
>

The U-B function type is the Urey-Bradley angle potential.  It is unrelated to 
dihedrals.  See the [angletypes] directive of ffbonded.itp and the manual for 
the proper format of U-B parameters.

-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

========================================