Hi Justin
I am using a CHARMM27 force field. I create a pdb file with the coordinates of my molecule and I create a .rtp and a .hdb file for this. I also edit atomtypes.atp, ffnonbonded.itp and residuetypes.dat The parameters for the parametrization are out of a supporting information of a paper that did MD with my molecule. The System is my molecule (isoalloxazine) in water. Do you want to see my .rtp file? Thanks you for helping me. 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 -- 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
