Hi So you think that I should edit something in ffbonded.itp? The parameters that I would write by hand in the topology should be supplemented in the ffbonded.itp?
I don't really know what I have to do concretely, to fix this problem. Greetings Lara ----- Ursprüngliche Message ----- Von: Justin A. Lemkul <jalem...@vt.edu> An: Discussion list for GROMACS users <gmx-users@gromacs.org> CC: Gesendet: 21:59 Sonntag, 6.Mai 2012 Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology On 5/6/12 3:45 PM, Lara Bunte wrote: > Hi > > You said: > >> The blank lines will be filled in with existing parameters from [angletypes] >> in ffbonded.itp. > I let the lines empty and I got an error at the first grompp, before energy > minimization. grompp missed this empty lines. Here a part out of the errors: > > ERROR 28 [file topol.top, line 229]: > No default Angle types > > > ERROR 29 [file topol.top, line 233]: > No default Improper Dih. types > > My system is a cofactor, the force field is CHARMM27, parametrized with data > out of a supporting information of a group that determined this parameters > for my cofactor by experiments and quantum mechanical calculations. In > residuetypes.dat I defined ISO Isoalloxazin. In the force field order I gave > all informations (I guess). > > What could be the problem? > > I am able to complete the topol.top file by hand, but I really like to know > what is the problem here. > A sequence of atoms in a topology (defined by atom type, not name or number) is mapped back to parameters in ffbonded.itp. If no suitable parameters are found, you get the error messages. In a normal topology (.top or .itp) for most force fields, the parameters are not explicitly stated because they are looked up in this manner. If you're introducing something new or overriding existing force field parameters, you need to explicitly include them in the topology or add them to the appropriate directive in ffbonded.itp. -Justin > > Thanks for help > > Greetings > Lara > > > > > > ----- Ursprüngliche Message ----- > Von: Justin A. Lemkul<jalem...@vt.edu> > An: Discussion list for GROMACS users<gmx-users@gromacs.org> > CC: > Gesendet: 20:34 Dienstag, 6.März 2012 > Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in > Topology > > > > Lara Bunte wrote: >> Hi >> >> In some lines the equilibrium angle and the force constant is missing.I give >> you an example: >> >> >> The [ angles ] section is build like >> >> [ angles ] >> ; ai aj ak funct c0 c1 c2 >> c3 >> 2 1 19 1 123.75 250.00 >> 1 2 3 1 123.75 250.00 >> 1 2 4 1 117.47 230.00 >> >> >> >> And my pdb2gmx output is for example something like >> >> [ angles ] >> ; ai aj ak funct c0 c1 c2 >> c3 >> 2 1 19 1 123.75 250.00 >> 1 2 3 1 >> 1 2 4 1 117.47 230.00 >> >> > > So you have a complete topology and one that has missing parameters, or are > you adapting an incomplete topology? > > What force field are you using? What is the system? For a normal protein > system, most force fields (all except Gromos, if I recall) produce bonded > directives with no parameters; they are looked up from ffbonded.itp and not > stated explicitly, so "missing" parameters are completely normal and not > problematic. If you're dealing with something nonstandard and you've had to > create .rtp entries, you'll need to post that information for diagnostic > purposes. > > In principle, there's nothing wrong with any of this. The blank lines will > be filled in with existing parameters from [angletypes] in ffbonded.itp. > These parameters are only overwritten if explicitly present in the topology. > If there is a bonded interaction referenced in the topology that does not > exist in ffbonded.itp, grompp will fail with a fatal error. > > -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 > > ======================================== > -- gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > 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 > > -- ======================================== 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 ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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? 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