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

Ye Yang knightyangpku at gmail.com
Thu Aug 18 20:18:17 CEST 2011

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"?
     Is there any suggestion how I can do that properly?
     Thank you very much.


2011/8/18 Justin A. Lemkul <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
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> ==============================**==========
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