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 <[email protected]> > > > 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 <[email protected] <mailto:[email protected]>> >> >> >> >> >> 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> >> > >> >> ==============================**__========== >> -- gmx-users mailing list [email protected] >> <mailto:[email protected]> >> >> >> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> >> <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> >> >> <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 [email protected] >> <mailto:gmx-users-request@**gromacs.org<[email protected]> >> >. >> >> Can't post? Read >> http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >> >> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > >> >> >> > -- > ==============================**========== > > 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 [email protected] > 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 [email protected]. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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