[gmx-users]Self-defined force-field problem, atomtype Nr not found
knightyangpku at gmail.com
Thu Aug 18 20:18:17 CEST 2011
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 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
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