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.
Ye 2011/8/18 Justin A. Lemkul <jalem...@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 | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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