Hi 2012/5/17 Lara Bunte <lara.bu...@yahoo.de>
> Hi > > Just for correct understanding: In this "empty" [ dihedrals ] bock are 11 > lines without equilibrium angle and force constant, that looks like: > > > [ dihedrals ] > ; ai aj ak al funct c0 c1 > c2 c3 c4 c5 > 2 1 19 8 2 > 6 8 9 10 2 > > > Did this mean, that this are really physical dihedrals, that were given by > pdb2gmx and the only reason that they are "empty" is, that they are not > parametrized? > Is this correct? > > No, it means that defaukt values (i.e. listed in [ dihedraltypes ] section ) will be applied > Greetings > Lara > > > > > > > > ----- 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 Donnerstag, 17.Mai 2012 > Betreff: Re: [gmx-users] Two [ dihedrals ] sections in topology > > > > On 5/17/12 10:48 AM, Lara Bunte wrote: > > Hi > > > > grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr > > > > gives me errors like > > > > ERROR 1 [file topol.top, line 233]: > > No default Improper Dih. types > > > > and so on. This line 233 is the starting of my empty [ dihedrals ] > block. I erase it by hand out of my topology, so that only the correct [ > dihedrals ] out of the .rtp and ffbonded.itp file are in the topology. > After this grompp works without error and even without any warning. > > > > > > So the question how to force pdb2gmx to use only my [ dihedrals ] block > is important for me, because I don't like to erase it always by hand out of > the topol.top file. > > > > This goes back to something that has been stated several times now, and > was discussed the other day. If pdb2gmx finds 4 atoms connected via bonds, > it assigns a dihedral to it. That's just physically real. If your force > field then doesn't have parameters for that particular interaction, you get > the error shown above. That doesn't mean you should go deleting things > until grompp "works" because what will result will likely be senseless. > > If your "empty" (which is not really empty, as we've been saying) > dihedrals are causing the problems, then you need to add parameters for > them in ffbonded.itp or in the topology itself, not hack the topology apart. > > -Justin > > -- ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > 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 > -- Cordiali saluti, Dr.Oteri Francesco
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