Hi Thanks for the answer. For me I don't know where the problem is.
>The .rtp file would be necessary to understand what is expected in the topology, as it is not clear to me why some lines have >explicit parameters while others do not. I put my .rtp file in the appendix. Could you please take a look on it? Greetings Lara ----- Ursprüngliche Message ----- Von: Justin A. Lemkul <jalem...@vt.edu> An: Discussion list for GROMACS users <gmx-users@gromacs.org> CC: Gesendet: 21:04 Mittwoch, 7.März 2012 Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology Peter C. Lai wrote: > [ angles ] is defined in ffbonded.itp. If you have new angles you will > need to specify them there. grompp will read ffbonded.itp and try to > correlate To be clear - [angles] can be specified in an .rtp file (but are not required, because pdb2gmx will by default generate all angles). An [angletypes] directive in ffbonded.itp supplies the parameters for angles. > it with the atomnumbers in the top file generated by pdb2gmx. If you modified > your top file by hand to include interactions which are missing from > ffbonded.itp then grompp will complain about missing interactions (at least > that is my experience). > Correct, but it is still not clear to me what the problem is here, if there is one. The .rtp file would be necessary to understand what is expected in the topology, as it is not clear to me why some lines have explicit parameters while others do not. -Justin > On 2012-03-07 05:19:19PM +0000, Lara Bunte wrote: >> 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 > -- ======================================== 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
LF.rtp
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