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

Ye Yang knightyangpku at gmail.com
Thu Aug 18 20:50:15 CEST 2011 

Oh, I see it now.
Even if I include all the needed terms in one file forcefield.itp, I need to
create files separated, using file name ffnonbonded.itp and ffbonded.itp?
Thank you very much

Ye

2011/8/18 Justin A. Lemkul <jalemkul at vt.edu>

>
>
> 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.
>
> -Justin
>
>      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://vt.edu/Pages/Personal/justin>
>>    <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
> MILES-IGERT Trainee
> 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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