[gmx-users]Self-defined force-field problem, atomtype Nr not found

Justin A. Lemkul jalemkul at vt.edu
Thu Aug 18 19:54:22 CEST 2011

Ye Yang wrote:
> Hi, everyone:
>      I am using a forcefield PACE(modified) from my friends.
>      Since there was a small program generating some dihedral terms 
> based on gromacs3.3.1, I need to use gromacs 3.3.1 to generate the 
> gromacs file.
>     Previously, for the npt/nvt, I was also using grompp (gromacs 3.3.1) 
> to generate the simulation file and run it in gromacs 4.5.4, it works 
> perfectly. However, I met some problem: since the pulling (constant 
> velocity or force)in gromacs 3.3.1 is totally different from gromacs 
> 4.5.4, I cannot use the same method, so I turned to grompp 4.5.4.
>     However, I met the same problem of "atomtype Nr not found each 
> time". It is the N of Arg in this force field
>     I have already created the folder in the 
> /home/yy58/gromacs/share/gromacs/top folder and tried gmx2pdb in gromacs 
> 4.5.4, which can create the gro file and top file (so as I see, it seems 
> the adding of the force field is correct.).
>     The folders PACE_13_NAMD.ff/ has the following files:
>     aminoacids.c.tdb  aminoacids.n.tdb  atomtypes.atp   forcefield.itp
> aminoacids.ddb    aminoacids.r2b    cg216water.gro  watermodels.dat
> aminoacids.hdb    aminoacids.rtp    cgWater.itp
>  I already included the itp file in the top file:
> in the top file, it indeed has:
>     ; Include forcefield parameters
> #include "PACE_13_NAMD.ff/forcefield.itp"
> Also in the forcefield.itp file, it has:
> Nr           16.000      0.000      A       0.0      0.0
> Similarly, in the file atomtypes.atp, aminoacids.rtp, the definition of 
> Nr also exists correctly (I have checked it and also use grompp to run 
> it in gromacs3.3.1, which does not have any trouble).
> Right now, I am really confused what is going on, could someone please 
> help me with this?

You are missing the ffnonbonded.itp and ffbonded.itp files, which causes your 
force field to break.  The ffnonbonded.itp file is the source of this particular 
error, since that is where grompp looks to find the nonbonded parameters for 
each atom type (among other things).



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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