Hi >Is there some reason to believe you should not have dihedrals? That doesn't >make much physical sense.
I want and have dihedrals in my topology. I don't want an additional empty dihedrals block in the topology. In my force field I gave impropers. Greetings ----- Ursprüngliche Message ----- Von: Justin A. Lemkul <jalem...@vt.edu> An: Lara Bunte <lara.bu...@yahoo.de>; Discussion list for GROMACS users <gmx-users@gromacs.org> CC: Gesendet: 17:02 Dienstag, 15.Mai 2012 Betreff: Re: [gmx-users] Two [ dihedrals ] sections in topology On 5/15/12 10:43 AM, Lara Bunte wrote: > Hi > > You wrote: > >> Two blocks of dihedrals are normal output for pdb2gmx - one for proper >> and one for improper dihedrals. > > > Is there a way to force pdb2gmx that there is only my block with improper > dihedrals in the topology? > Normally pdb2gmx will generate proper dihedrals based on bonded connectivity. Is there some reason to believe you should not have dihedrals? That doesn't make much physical sense. > > Could that be a problem in further calculations, i.e. energy minimization if > there is this empty [ dihedrals ] block in the topology? > What you've been defining as "empty" is not necessarily so. The fact that parameters are not explicitly printed is not inherently indicative of a problem, since the parameters are looked up from ffbonded.itp and not necessarily recapitulated in the topology. If you get fatal errors about missing parameters, that's a separate issue. > >>> [ bondedtypes ] >>> ; bonds angles dihedrals impropers >>> 1 1 5 5 >> >> Those are angle, dihedral and improper function types that are abnormal >> for CHARMM27. Using these in your .rtp means that you are no longer >> using CHARMM27. It might be reasonable for you to do this, but you need >> to be absolutely sure why. Importing a topology from another force field >> is not an acceptable reason. > > What would be the correct numbers in the [ bondedtypes ] for using CHARMM27 > force field? > Look in charmm27.ff/aminoacids.rtp. -Justin -- ======================================== Justin A. Lemkul, Ph.D. 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