Hi All needed parameters for [ angles ] in the topology are defined in my .rtp file parametrization and also in the ffbonded.itp in the CHARMM27 folder. This still don't work. In the topology my [ angles ] block looks like
[ angles ] ; ai aj ak funct c0 c1 c2 c3 2 1 19 1 1 2 3 1 123.75 250.00 1 2 4 1 117.47 230.00 3 2 4 1 2 4 5 1 115.95 105.00 So there are lines missing. In my ffbonded.itp angles are all defined like [ angletypes ] ; i j k func th0 cth ub0 cub ; f5: Urey-Bradley NN3A CN1A ON1 5 123.75 250.00 NN3A CN1A NN2U 5 117.47 230.00 CN1A NN2U HN2 5 115.95 105.00 And in my .rtp file it looks like ; Col 1: angle classification ; Col 2: equilibrium bond angles in degrees ; COl 3: force constant in kcal/(mol*rad^2) [ angles ] N1 C2 O2 123.75 250.00 N1 C2 N3 117.47 230.00 C2 N3 H3 115.95 105.00 What is the problem? Why are there still this missing lines in the topology? Thanks for helping me Greetings Lara ----- Ursprüngliche Message ----- Von: Justin A. Lemkul <[email protected]> An: Discussion list for GROMACS users <[email protected]> CC: Gesendet: 20:59 Montag, 7.Mai 2012 Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology On 5/7/12 2:54 PM, Lara Bunte wrote: > 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. > > If the parameters are not already present in the force field, you have 2 options: 1. Add them to ffbonded.itp - useful if you have multiple molecules that you need to simulate 2. Add them to the topology - the easiest approach Both effectively accomplish the same thing, but approach #2 is slightly more straightforward and does not potentially affect all your simulations should something go wrong. -Justin > Greetings > > Lara > > > > > > ----- Ursprüngliche Message ----- > Von: Justin A. Lemkul<[email protected]> > An: Discussion list for GROMACS users<[email protected]> > 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<[email protected]> >> An: Discussion list for GROMACS users<[email protected]> >> 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 [email protected] >> 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 [email protected]. >> 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 [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
