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

Justin A. Lemkul jalemkul at vt.edu
Thu Aug 18 20:21:15 CEST 2011

Ye Yang wrote:
> Hi, Justin:
>      Thank you for the reply.
>      But I am not sure for gromacs 4.5.4. since for gromacs 3.3.1, I 
> only need one itp file for my forcefield. Should I just split this 
> forcefield.itp file into two different part, and write a new 
> forcefield.itp which says "#include ffnonbonded.itp, #included 
> ffbonded.itp"?

That's all the forcefield.itp file has ever done, really.  It defines the 
default interaction types for the system and #includes the relevant bonded and 
nonbonded parameters.  Maybe that's what your forcefield.itp file does, but in 
the file listing, you did not have ffnonbonded.itp and ffbonded.itp.  These 
files are where grompp gets the bulk of its information and without them will be 
hopelessly broken.  All required input files are described in the manual, Chapter 5.


>      Is there any suggestion how I can do that properly?
>      Thank you very much.
> Ye
> 2011/8/18 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>     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
>     -- 
>     ==============================__==========
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     <tel:%28540%29%20231-9080>
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>     ==============================__==========
>     -- 
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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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